About The IUPHAR/BPS Guide to PHARMACOLOGY

Background

For more information on the Guide to PHARMACOLOGY (abbreviated as GtoPdb) see the About page and the FAQ. The Guide to PHARMACOLOGY is based on information previously available separately in the International Union of Basic and Clinical Pharmacology Database (IUPHAR-DB) and the Guide to Receptors and Channels (GRAC). This help page describes the terms and symbols used in the database and the search tools available on the website.

Terms and symbols

For further information on the pharmacological terms mentioned see the NC-IUPHAR publication on terms and symbols. Please refer also to the Glossary section of this help page.

Tutorial

A tutorial for using the database and guidance on navigating the website is available to download as a PDF.

Contact us

If you would like to get in touch with any comments, questions, error reports and suggestions please email us.

How to cite

Please refer to this page for details on how to cite the information contained in the Guide to PHARMACOLOGY.

About IUPHAR-DB and GRAC

The information in the Guide to PHARMACOLOGY builds upon two previously available resources:

1. IUPHAR-DB (www.iuphar-db.org) was developed from 2003-2014 under the auspices of NC-IUPHAR (International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification) to provide an accurate educative resource to the scientific community. These data constitute the detailed target pages on the GtoPdb site. It relies on contributions by expert pharmacologists who volunteer their time. All contributors are attributed near the bottom of the relevant database pages. A full contributor list can be viewed here.

2. The Guide to Receptors and Channels (GRAC) published in the British Journal of Pharmacology:

SPH Alexander, A Mathie, JA Peters. (2011) Guide to Receptors and Channels (GRAC), 5th edition. Br. J. Pharmacol., 164 (Suppl. s1), 1-324.

The Concise Guide to PHARMACOLOGY replaces GRAC and represents a biennial snap-shot view of the concise family pages from the Guide to PHARMACOLOGY website.

The Data in the Guide to PHARMACOLOGY

The data are primarily summarised from selected primary literature articles, which are linked to PubMed. Where possible the data are linked to other relevant databases for further information.

Entry points to the data are either via the database search tools (quick search at the top of every page or 'Advanced Search' tools linked from the menu) or through browsing the target and ligand lists. Targets are organised into protein classes (GPCRs, enzymes, ion channels etc) and then subdivided into families (e.g. Adenosine receptors).

Each family page contains a summary of the main properties and the recommended nomenclature and key ligands for each target, as well as a further reading list. This "concise" view of the information for each family serves as a useful "at-a-glance" introduction to the family and to each target.

For the most important targets links are provided to more detailed pages including a longer introduction to the family and detailed pages for each target. Target pages are modelled on IUPHAR-DB pages, with expert-curated information on the nomenclature, genetic, structural, pharmacological, functional, physiological, and clinical properties.

Links are also provided where relevant to further information and the chemical properties of ligand molecules.

Downloading Data and Documents

We provide selected data files available for download on this page. These are the most commonly requested file formats. We may be able to provide other formats if you email us. We also provide SQL dump files of the full database. The licenses covering reuse of the data are very generous and permit both commercial and non-commercial use with attribution.

Our REST web services and API are intended to provide programmatic access to the data in JSON (JavaScript Object Notation) format, which is easy to read for both humans and computers. Web services are updated at each database release and any changes in the database structure will be reflected in the JSON output. A full listing and examples for using the web services are provided here.

We also provide slide sets and posters including a generic slide set for public use when producing presentations and teaching materials on the Guide to PHARMACOLOGY. The current version can be accessed here.

Search Facilities

A quick search box is provided at the top all the main pages. To search for a target, family or ligand start typing the name in the query box and the search function will start looking for matching entries in the database. If any are found they will be displayed as a drop-down list. Clicking on a matching name takes you straight to its database page. Alternatively, type the whole phrase and press "Search database" to perform a complete database search.

You can restrict your search or perform different types of searches, e.g. by database identifier, literature reference, or chemical structure, using the advanced search tools. These can be accessed from the drop down menu on the main menu bar. Advanced search tools include different search options such as restricting text searches to specific database fields or target types, or performing searches by accession number or chemical structure. Depending on the type of data you wish to search for you can choose between target search tools and chemical search tools.

Target search tools

  • Target text search: perform keyword searches of selected database fields.
    1. Type the search term(s) into the text box.
    2. If multiple words are entered they must all be present for a result to be returned.
    3. Select the field(s) from the list that you wish to search.
    4. To select multiple fields hold down CTRL while selecting the fields.
    5. To search the entire database select 'All' at the top of the field list.
    6. You can optionally choose to limit your results by species and target type.
  • Search by database identifier: retrieve targets by entering an external database identifier or a gene name, e.g. Entrez gene id or HGNC approved name.
    1. Type the identifier into the text box.
    2. Select the source database from the drop-down list.
    3. Multiple identifiers can be searched by separating them with spaces. If they are from different source databases, select 'Unknown' in the database list.
  • Search for literature references: search for families where a particular literature reference appears.
    1. Type a keyword, article title, author last-name or PubMed Id into the text box.
    2. Select the type of query to perform from the drop-down list.
    3. Multiple PubMed identifiers may be entered separated with spaces.
  • Search for targets by sequence: perform a sequence-based search for targets using BLAST.

    The BLAST tool allows you to BLAST a sequence against the targets in the Guide to PHARMACOLOGY database. You may supply either a polypeptide sequence or a nucleotide sequence, which will be automatically translated in all possible frames before querying. You have the option of supplying either FASTA sequences or plain text sequences, and the sequence can be pasted directly into the search box or uploaded from your local file system.

    You can filter the results you get back by species, control the maximum number of hits and number of hits per page, and also specify a maximum E-value (expect value) for your query – the larger this E-value, the more distantly related the sequences it returns will possibly be.

    Once the results are displayed, the aligned sequences will by default be coloured according to residue, but this can be disabled.

Ligand search tools

  • Ligand name search: retrieve compounds by matching to their name. Also (optionally) searches in target interaction comment fields (agonists, antagonists etc) for matches.
    1. Type the search term(s) into the text box.
    2. If multiple words are entered they must all be present for a result to be returned.
    3. Check the box to include searches on comment fields or uncheck to exclude.

  • Search by database identifier: retrieve compounds by entering an external database identifier, e.g. PubChem CID or ChEBI id (in this case the number must be prefixed with "CHEBI:").
    1. Type the identifier into the text box.
    2. Select the source database from the drop-down list.
    3. Multiple identifiers can be searched by separating them with spaces. If they are from different source databases, select 'Unknown' in the database list.

  • Chemical structure search: search for compounds by chemical structure. Performs substructure, SMARTS, similarity and identity (exact) searches.

    Substructure
    This search uses the Dotmatics Pinpoint algorithm to match a drawn 2D/Markush structure and returns any compounds which contain the query structure.
    SMARTS
    Uses Pinpoint for matching Daylight SMARTS and returns any compounds which match the query.
    Similarity
    Similarity search uses the Tanimoto coefficient to compare the similarity between the query molecule and molecules in the database using Pinpoint generated expanded fingerprints and returning all molecules above a user selected threshold (>70% or 85%).
    Please note: if your similarity search does not return appropriate results please try using the substructure function. (We are currently working on optimising our similarity search.)
    Exact
    Exact match query returns all compounds matching the canonical SMILES, with no regards to the chiral specification. This is attained by Tanimoto comparison of fingerprints and returning all with 100% similarity.

    Usage
    1. Either: enter a SMILES or SMARTS representation of the chemical structure into the text box and press 'Import SMILES/SMARTS' to load the structure into the editor.
    2. Or: draw the chemical structure into the editor. The icon in the top right above the atoms can be used to add other atoms, R groups and SMARTS groups.
    3. Choose the type of search to perform from the drop-down menu on the top right (e.g. similarity - high).
    4. Choose the type of chemical class to search for (recommended type is small molecules but you can also search for peptides with SMILES available).
    5. The returned structures are roughly ordered according to their flexibility/complexity.
    6. On the results page, clicking on a ligand's image or name will take you to its ligand page. Clicking on the 'Use in search' button will load the ligand into the editor so it can be modified if required and used in a further search.

    Notes
    1. Currently the search function does not consider chiral specification of matched compounds. This is to ensure that all relevant results will be returned. Please ensure that your input structure does not include chiral or isotopic specification, otherwise exact match, substructure and SMARTS searches may miss relevant structures.
    2. Exact match, substructure and SMARTS searches are currently not able to recognise alternative tautomers that may be in the database. Please use similarity searching if you suspect this could be occurring.

Concise Family Pages

For all targets; additional information relevant to specific target types is listed below this section.

Overview - Provides a brief introduction to the target family. For targets where a more comprehensive introduction may be available, a link is provided to the relevant page.

Nomenclature - The recommended nomenclature for a structurally and operationally distinct target in a given family. Where this is the NC-IUPHAR published recommended nomenclature, this is specified in the Overview section with references to the relevant articles in Pharmacological Reviews. In cases where there are no published NC-IUPHAR recommendations, the adopted nomenclature is usually one of: the HGNC approved gene name, a name commonly used in the literature or a preliminary recommendation from NC-IUPHAR.

Other names - Details a list of alternative names that exist in the literature, but are not the recommended nomenclature.

More detailed page - Links to the more detailed target page.

Subunits - Lists the subunits that together make up the homomeric or heteromeric protein.

Genes, UniProt and Ensembl IDs - For each target, the human (Hs), mouse (Mm) and rat (Rn) gene symbols are provided with links to the HUGO Gene Nomenclature Committee (HGNC), Mouse Genome Informatics (MGI) and Rat Genome Database (RGD) web sites. Links are also provided to the Ensembl genome database and the UniProt protein knowledgebase. Further database links can be accessed via the more detailed target pages. For descriptions of databases linked to see the Database Links table.

Rank order of potency (certain targets) - Details the order of potency of the activity of a series of ligands at a particular target.

Ligand interaction data - Ligand interactions at targets are listed by ligand action, selectivity and ligand context. Where a ligand is endogenous for the target tested, this is indicated accordingly. Ligand names are clickable links to pages describing the ligand's properties (see the Ligand Page section). Ligands are chosen to represent a set of available recommended agonists, antagonists, activators, inhibitors, blockers, allosteric regulators and probes for particular targets. Where possible a summary of the literature recording the ligand's activity are provided.

Comments - Includes additional comments and information about the target family and data presented in the tables.

Further reading - A selection of background literature on the target family.

References - An alphabetical list of references cited in the target family pages.

N.B. The concise family pages focus on the properties of human targets and data referring to other species are indicated accordingly.

Detailed Target Pages

Nomenclature - The recommended nomenclature for a structurally and operationally distinct target in a given family. Where relevant this is the NC-IUPHAR recommended nomenclature published in Pharmacological Reviews. In cases where there are no published NC-IUPHAR recommendations, the adopted nomenclature is usually one of: the HGNC approved gene name, a name commonly used in the literature or a preliminary recommendation from NC-IUPHAR. See the relevant target section below for further information.

Colour codes - Each target page and introduction are given a colour code to indicate the status of their annotation:

image of a green circle Annotated and expert reviewed
Data have been annotated and reviewed by an expert. Please contact us if you can help with updates.
image of an orange circle Annotated and awaiting review
Available data have been entered by experts or curators but are yet to be reviewed by independent experts. Please contact us if you can help with reviewing.
image of a grey circle Awaiting annotation/under development
These pages are awaiting annotation. A minimum amount of data are displayed about receptors, e.g. nomenclature and database links. Whilst some pages are under development, others still need volunteers so please contact us if you can help with annotation.

Gene and Protein Information - For human, mouse and rat targets the following data are displayed:

Column Definition
Transmembrane domains (TM) The number of times the polypeptide passes through the cell membrane.
P loops (Some ion channels only) The number of pore loops in the protein.
Amino acids (AA) The number of amino acids which make up the protein.
Chromosomal location The genetic location of the encoding gene.
Gene symbol The official symbol given to the gene that codes for the target which, if highlighted in blue, links to either the HGNC, MGI or RGD databases.
Gene name The full name of the gene that codes for the target.
Reference A reference to the first paper(s) describing the cloning of the target.

Previous and Unofficial Names - Alternative names that exist in the literature or other databases, but are not the current recommended nomenclature. Also includes any previous gene symbols or names used for human, mouse or rat genes.

Database Links - Links are provided to other relevant resources, including genomic databases (e.g. Ensembl, Entrez Gene), protein databases (e.g. RefSeq, Uniprot) and others such as ChEMBL (MedChem literature data on drug-like molecules and their targets) and DrugBank (data on approved drugs and the proteins they interact with). For a full list and descriptions see the Database Links table.

Selected 3D Structures - Highest resolution structures were selected and an attempt was made to include for each target the unliganded, agonist, and antagonist bound structures where available. Links are provided to associate ligands with RCSB PDB ligand pages where possible.

Natural/Endogenous Ligand(s) - The principal endogenous or natural ligand(s) for the target.

Ligands - Ligands are arranged in tables according to their action at the target.
The column headings or icons in the ligand table are described below:

Icon/Table heading Definition
Small molecule or natural product Indicates that a ligand is either a small organic molecule (synthetic or naturally occurring) or a natural product (or derivative).
Peptide Indicates that a ligand is a peptide (synthetic or naturally occurring) or antibody.
Approved drug Indicates that the ligand is or has in the past been approved for human clinical use by a regulatory agency.
Primary target Indicates that the target may be considered the primary target of the compound. In some cases, e.g. dual inhibitors, a compound may have more than one primary target.
Selectivities Indicates that there are data available for the ligand binding to other targets in the database.
Clicking on this icon displays the list of targets and the ligand's potency at each target.
Endogenous Indicates that the ligand is endogenous in the species of the target under test.
Labelled Indicates that the ligand is chemically labelled such as with an unstable isotope, fluorescent tag or small chemical entity.
Radioactive Indicates that the ligand is labelled with a radioactive isotope.
Immunopharmacology Indicates that the ligand has been tagged in the database as being relevant to immunopharmacology.
Hs, Mm, Rn Indicates the species of the target and NOT the species of the ligand. '?' indicates that the species was not given in the original publication. Selectivity tables are not shown when the species is unknown. Mouse-over the short name to see the longer species name.
Ligand The name of the ligand, which can be clicked on to open a ligand page. Ligand pages include database links, alternative names, data on affinity for other targets, structural information and links to similar ligands, where available.
Action This indicates how the ligand binds to the target (see the terms and symbols document for a definition of the terms).
Affinity A measure of how strongly the ligand binds to the target. In cases where no binding data are available functional data may be used.
Units The units used to measure the ligand's binding to the target (see the terms and symbols document for a definition of the terms).
Concentration range Where affinity data are not available, the concentration range of ligand used for the study is displayed (in M).
Holding voltage The voltage at which the displayed affinity was determined (in mV). 'Physiological' indicates that the experiment was performed in intact cells where voltage could not be determined.

The ligands can be sorted in alphabetical order or by action, affinity, unit, concentration range or holding voltage by clicking on the column header.

Screening Data - Where there are large scale ligand screening data in the database, these are included in separate tables. Usually a cut-off value is applied so that only ligands with activities below a particular concentration will be displayed on the target page and a link is given to the full set of data for the target. Where the screen tested multiple variants of the target the data for the variants are displayed in separate tables. Similarly, on ligand pages the screening data are displayed in separate tables, with targets ordered by activity level.

Functional Assay - Details of pharmacological test systems (whole tissues or isolated cells) in which a response can be firmly attributed to the function of a defined receptor type.

Tissue Distribution - Central and peripheral distribution of the receptor (and the identifying techniques).

Expression Datasets - Graphical displays of selected high-throughput expression datasets.

Physiological Functions - The physiological response mediated by the receptor if established in whole tissue, preferably in vivo.

Physiological Consequences of Altering Gene Expression - Important physiological differences observed as a result of modifying expression levels (e.g. knockouts).

GPCRDB Experimental Mutation Data - Data on experimentally generated mutations from literature are provided for GPCRs by GPCRDB. GPCRDB is working with a consortium to collate data on GPCR mutants and is inviting submissions. Thus, the mutation data displayed here will update automatically whenever GPCRDB release new data.

Phenotypes, Alleles and Disease Models - Additional data on "spontaneous, induced and genetically-engineered mutations and their strain-specific phenotypes" from Mouse Genome Informatics.

Clinically-Relevant Mutations and Pathophysiology - Details of the pathophysiologies in which the receptor is involved, including, where available, the ligands at the receptor which are of therapeutic use. Details are provided of individual mutations that lead to the pathophysiology, in terms of the change in the amino acid sequence.

Gene Expression and Pathophysiology - The pathophysiology that arises from abnormal gene expression.

Biologically Important Receptor Variants - Details of polymorphisms and post-transcriptional modifications (e.g. splice variation) that influence function. Where possible links to the protein and nucleotide sequences are provided.

N.B. additional species are sometimes used where data for human, rat and mouse are unavailable, the most common are: Bt (bovine), Oc (rabbit), Cp (guinea pig), Clf (dog).

GPCR Pages

Concise pages

Nomenclature - The NC-IUPHAR recommended nomenclature for a structurally and operationally distinct receptor or subunit in a given family. NC-IUPHAR publishes its recommended nomenclature in Pharmacological Reviews. In cases where no publication yet exists this is the preliminary recommendation from NC-IUPHAR.

Principal Transduction - The preferred principle receptor signalling pathway or mechanism, where established.

More detailed pages

Primary and Secondary Transduction Mechanisms - The preferred primary and secondary receptor signalling pathways or mechanisms, where established.

Ligands - Ligands are categorised as agonists, antagonists or allosteric regulators.

Ion Channel Pages

For voltage-gated (VGIC), ligand-gated (LGIC) and other types of ion channels

Concise pages

Nomenclature - The NC-IUPHAR recommended nomenclature for a structurally and operationally distinct receptor or subunit in a given family. NC-IUPHAR publishes its recommended nomenclature in Pharmacological Reviews. In cases where no publication yet exists this is the preliminary recommendation from NC-IUPHAR.

Ligand interaction data - In some cases ligand interactions at ion channels are listed under the subunit that confers specificity to the heteromeric channel (e.g. nicotinic acetylcholine receptor alpha subunits). Additional supporting information is provided such as subunit/homomer/heteromer selectivity, ligand context and receptor site of action.

Functional characteristics - Provides details of the conductance, voltage-dependence, rectification and selectivity properties of ion channels.

More detailed pages

Associated Proteins - Proteins that interact directly with the receptor either as heteromeric pore-forming subunits, auxiliary subunits or associated proteins.

Ion Selectivity and Conductance - This table displays relative or absolute conductance data for the receptor on a 'per species' basis.

Voltage Dependence - (VGICs only) This table displays the voltages of activation, inactivation and deactivation and the relevant time constants, where available.

Ligands - For LGICs, ligands are categorised as agonists, antagonists, channel blockers or allosteric regulators. For VGICs, ligands are categorised as activators, channel blockers or gating inhibitors, according to the following definitions:

Activators
Ligands that activate ion channels by binding directly to them, including ligands that cause a change in the voltage dependence of channel gating that favors activation.
Gating inhibitors
Ligands that inhibit ion channel gating by directly binding to the channels, including ligands that inhibit ion channel activation and those that inhibit ion channel inactivation.
Channel blockers
Ligands that block ion movement through the pore of ion channels.

Nuclear Receptor Pages

Concise pages

Nomenclature - Typically the most commonly used name for the receptor.

Systematic Nomenclature - The Nuclear Receptor Nomenclature Committee (NRNC) recommended name for the receptor. See reference:
Nuclear Receptors Nomenclature Committee (1999). A unified nomenclature system for the nuclear receptor superfamily. Cell 97, 161-163. [PMID:10219237]

More detailed pages

Ligands - Compounds that bind reversibly to NRs into the C-terminal ligand binding pocket (LBP).

Agonists
Ligands that induce an active conformation of the receptor.
Antagonists
Ligands that produce a conformation and an action of the receptor distinct from that produced by an agonist.
Inverse agonists
Ligands that can promote corepressor recruitment.
Partial agonists
Agonists that in a given tissue, under specific conditions, cannot elicit as optimal an effect (even when applied at high concentration, so that all the receptors should be occupied) as can another agonist acting through the same receptors in the same tissue.

Unliganded receptor - Considered preferable compared with apo-receptor.

DNA Binding - Hormone response elements (HRE) are DNA recognition sites which include inverted repeat DNA half sites and direct repeats (e.g. DR1-DR5) for homodimeric and heterodimeric receptors respectively.

Co-binding Partners - Proteins which specifically interact with and induce a functional effect with NRs.

Co-regulators - Macromolecules that associate with NRs to modulate their transcriptional activity; divisible into coregulators that promote positive activity (coactivators) and those that promote negative activity (corepressors).

Main Target Genes - Genes regulated directly by the actions of NRs.

Transactivation - Activation of transcription by the binding of a transcription factor (and coregulators) to a DNA regulatory sequence.

Isoforms - Products of the same gene produced by alternative splicing, alternative promoter usage, alternative translational initiation; does not consider post-translational modifications; examples: RARα1 and RARα2.

Terms and definitions were adapted from the IUPHAR Compendium.

Catalytic Receptor Pages

Concise pages

Nomenclature - The nomenclature used here is either recommended by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) (based on the Enzyme Commission (E.C.) number system), is the HGNC approved name or is based on nomenclature in common use in the literature.

Abbreviated Name - An abbreviated name commonly used in the literature.

Systematic Name - A systematic name used by HGNC or inthe literature.

Endogenous Ligands - Ligands originating from within the studied organism shown to have activity at the receptor.

Adaptor Proteins - Cytoplasmic-based proteins containing protein-binding modules involved in catalytic receptor signalling.

E.C. Number - See below description for enzymes.

Enzyme Pages

Concise pages

Nomenclature - The nomenclature used here is either recommended by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) (based on the Enzyme Commission (E.C.) number system), is the HGNC approved name or is based on nomenclature in common use in the literature.

Common Abbreviation - Typically the most commonly used abbreviation for the enzyme name as used in the literature; not necessarily the preferred abbreviation.

E.C. Number - A Enzyme Commission (E.C.) number is a numerical-based classification system for an enzyme based on the reaction it catalyses. Each E.C. number consists of a four-number code, with the first number describing one of 6 possible general enzyme functions: oxidoreductases, transferases, hydrolases, lysases, isomerases or ligases, with the remaining numbers used as an increasingly precise classifier for the enzyme reaction. As E.C numbers describe enzyme function, an E.C number is not necessarily unique to a given enzyme, i.e. an E.C number may be assigned to more than one enzyme, and an enzyme with more than one function may be assigned several E.C numbers.

Substrate/Endogenous Substrate - The substance which a particular enzyme binds to and converts to product. An endogenous substrate originates from the organism in which the given enzyme is being studied, while synthetic substrates include drugs and other non-naturally occurring chemical agents.

Product - The substance arising from conversion of a substrate by an enzyme.

Inhibitor/Endogenous Inhibitor - A substance that reduces or prevents the activity of the enzyme, usually by binding to the enzyme. Enzyme inhibitors may be reversible or irreversible, and reversible inhibitors are competitive or non-competitive. Endogenous inhibitors originate from within the organism in which the enzyme is being studied, while synthetic inhibitors include drugs and other non-naturally occurring chemical agents.

Activator/Endogenous Activator - A substance that increases enzyme activity after binding to the enzyme.

Cofactor - A chemical substance that binds to the enzyme and is required for its activity. Cofactors are non-peptides, and may be organic or inorganic compounds.

More detailed pages

Km - The Michaelis constant (Km) defines the concentration of substrate when the reaction rate is half of Vmax.

Vmax - The maximal rate of reaction, or maximal velocity reached by the system when under conditions of maximum (saturating) concentrations of substrate.

Transporter Pages

Nomenclature - Typically the most commonly used name for the transporter.

Systematic Nomenclature - The recommended name for the transporter as originally described in a series of reviews published in Pflügers Archives 447, Number 5, February 2004. [PMID:14624363]

Common Abbreviations - Commonly used abbreviations of the transporter that exist in the literature.

Other Names - Alternative names that exist in the literature, but that are not the recommended nomenclature.

Substrates/Endogenous Substrates - Details a list of the substances that are transported. Where the substrate is endogenous for a particular transporter, this is indicated accordingly. Substrate names are clickable links to pages describing the substrate's properties.

Inhibitors/Selective Inhibitors - The inhibitors of a transporter's ability to translocate substrates across the membrane. Where the inhibitor is selective for a particular transporter, this is indicated accordingly. Inhibitor names are clickable links to pages describing the inhibitor's properties.

Functional Characteristics - Provides details of the conductance, voltage- and time-dependence properties of transporters.

Stoichiometry/Predicted Stoichiometry - Provides details of the experimentally measured or predicted substrate binding stoichiometry of the transporter together with the direction of substrate translocation across the membrane.

Ligand Pages

2D Structure - An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

Calculated Physico-chemical Properties - Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand:

Number of Hydrogen Bond Acceptors
Number of Hydrogen Bond Donors
Number of Rotatable Bonds
Molecular Weight
Topological polar surface area
Polar surface area (PSA) is defined as the surface sum over all polar atoms (usually oxygen and nitrogen), including also attached hydrogens. Topological polar surface area is a useful parameter (molecular descriptor) employed for optimising cell permeability by medicinal chemists. It is generated by a computation of functional group contributions. For details on the methodology used see
Ertl, P., Rohde, B., and Selzer, P. (2000) Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 43, 3714–3717.
XLogP
Log of partition coefficient (LogP) is the logarithm of the ratio of concentrations of un-ionized compound between two solutions (octanol and water). The prediction of LogP is based on the atom-type method called XLogP as implemented in KNIME. For details of the methodology see
Wang, R., Fu, Y., and Lai, L. (1997) A New Atom-Additive Method for Calculating Partition Coefficients. Journal of Chemical Information and Computer Sciences. 37, 615-621.
No. Lipinski's rules broken
Lipinski's Rule of Five is a rule of thumb to evaluate ‘druglikeness’, or determine if a chemical compound with a certain pharmacological or biological activity has properties that would make it a likely orally active drug in humans. For further details see
Lipinski, C.A., Lombardo, F., Dominy, B.W., and Feeney, P.J. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Del Rev. 23, 3–25.

Ligand classification - Compounds are assigned to general classes based on their origin and structural properties. See the glossary for a list of classes and definitions.

Approved drug - Indicates pharmacologicaly active substances, specified by their INNs, that have been approved for clinical use by a regulatory agency, typically the FDA, EMA or in Japan. This classification persists regardless of whether the drug may later have been withdrawn or discontinued. (N.B. in some cases the information on approval status was obtained indirectly via databases such as Drugbank.)

Withdrawn drug - No longer approved for its original clinical use, as notified by the FDA, typically as a consequence of safety or side effect issues.

Discontinued drug - No longer marketed for routine clinical use but not withdrawn because of negative effects. Typically these have been superceeded by newer, more effective drugs.

Prodrug - Substance covalently changed into an active drug after administration, via active metabolism or passive hydrolysis. Prodrugs can be inactive. Both approved prodrug and drug will have different INNs while development prodrugs and drugs may have different code names. Prodrugs are linked to drug database pages and vice versa.

DrugBank drug categories are also provided where possible.

IUPAC name - A systematic chemical name generated according to IUPAC rules using the NCI/CADD Chemical Identifier Resolver

Synonyms - Alternative names that exist in the literature, which may include systematic names.

International Nonproprietary Name (INN) - The official nonproprietary or generic name given to a pharmaceutical substance, as designated by the World Health Organization (WHO). Substances where this compound is an active ingredient are listed.

Species and Gene/Precursor (endogenous peptides) - Species refers to the organism(s) which naturally produce the peptide. Species information is linked to the encoding genes and protein precursor(s) for the peptide (genes and precursors are described for human, rat and mouse where applicable, or other relevant species). A single ligand entry is made where the mature peptide sequence is identical across multiple species. If there is peptide sequence variation across multiple species, then separate ligand entries are made for each species with a different sequence.

Database Links - Provides the accession number and link outs for selected chemical databases, including PubChem, DrugBank, ChEBI and PDB. For a full list and descriptions see the Database Links table. CAS Registry Numbers are provided where known. CAS Registry Number is a Registered Trademark of the American Chemical Society. Peptide ligand tables include links to genomic and protein databases.

This section includes a new option to display the results for an InChIKey search in Google, the utility of which has recently been described (Southan 2013). While the entire Key is used for exact-match searches of ChemSpider, the Google search uses just the inner "layer" of 14 characters approximating to the basic molecular connectivity. It will thus retrieve all related entries with isomeric differences encoded in the outer layer of the key. The results, typically returned in less that 0.5 seconds with very high specificity, are collated from over 50 million InChIKeys cached by Google from a comprehensive range of databases and web resources. See reference: Southan C (2013). InChI in the wild: an assessment of InChIKey searching in Google. J Cheminform. 5, 10. [PMID:23399051]

Biological Activity - Tables of selectivity at targets in the database. Data are separated by target type (GPCR, ion channel, NHR, enzyme, catalytic receptor, transporter, other protein target) and by species.

Natural/Endogenous Targets - Targets where the ligand acts as the principal endogenous or natural ligand.

Enzymes/Transporters - Where the chemical is part of an enzyme reaction annotated in the database or is known to be a substrate for a transporter protein in the database, these are listed.

Screening Data - Where there are large scale ligand screening data in the database, these are included in separate tables. Usually a cut-off value is applied so that only targets where the ligand has activity below a particular concentration will be displayed on the ligand page and a link is given to the full set of targets in the screen. Where the screen tested multiple variants of a target the data for the variants are displayed in separately.

Summary of Clinical Use - Overview of the principal uses of approved drugs in the clinic. Lists the condition(s) for which the drug is used, or has been used, to treat. In the case of drugs with multiple targets, this field may indicate which of these targets is the main therapeutic target.

Mechanism Of Action and Pharmacodynamic Effects - Pharmacodynamics is the study of the biochemical and physiological effects of drugs on the body and examines the mechanisms of drug action, including the relationship between drug concentration and effect.

Pharmacokinetics

Absorption/Distribution
Consideration of the factors which affect how much an administered drug gets into the bloodstream and how much is available at its effector (i.e. bioavailability at the drug target). For orally administered drugs, compound solubility, gastric emptying time, intestinal transit time, chemical instability, and ability to cross gut mucous membranes all need to be considered. If these obstacles are insurmountable another route of administration must be found.
Metabolism
The mechanisms by which the body breaks down drugs. For most small-molecule drugs metabolism is performed by the cytochrome P450 redox enzymes in the liver.
Elimination
The routes via which the body eliminates drugs and their metabolites.
Population pharmacokinetics
The effects of the drug in specific groups, based on age, gender, race or weight or in populations with pre-existing conditions, or otherwise requiring special consideration (such as paediatric geriatric populations).
Organ function impairment
Dosing considerations in populations with specific organ impairment, especially in patients with renal and hepatic insufficiency as these conditions may disturb metabolism and elimination and thereby affect the total bioavailability of the drug. In such groups dose adjustments may be necessary.

ADME links - links to detailed information on ADME properties.

Structure Downloads - Various representations of the ligand 2D molecular structure, generated using Open Babel. These are:

SMILES (Simplified Molecular Input Line Entry Specification)
A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.
Standard InChI (IUPAC International Chemical Identifier) and InChIKey
InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Peptide Structure - Peptide ligand pages contain information on the peptide sequence (one and three letter amino acid sequences) with post-translational and chemical modifications detailed where relevant. Where appropriate post-translational and chemical modifications are represented in the three letter amino acid sequences.

Similar Ligands (small molecules) - Similar ligand sets were generated using a clustering algorithm implemented in Pipeline Pilot (Accelrys, San Diego, CA, USA).

Related Sequences (peptides) - Currently this table lists other peptides in the database that have the same parent precursor protein, as well as corresponding peptides from other species, if they are in the database.

Other Similar Sequences (peptides) - This table lists peptides in the database with similar sequences, which may include synthetically-derived and endogenous peptides that are not derived from the same gene or its orthologues. Sequences were clustered using the program h-cd-hit available from the CD-HIT Suite. Peptides were first clustered at a high identity (90%) and the non-redundant sequences were further clustered at a low identity (60%). For details of the methodology see
Ying Huang, Beifang Niu, Ying Gao, Limin Fu and Weizhong Li. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 26, 680-682.

Ligand Activity Visualisation Tool

This tool provides charts with box plots summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. It is currently only available for ligands that have an entry in ChEMBL. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

Filtering ChEMBL data - activity data are extracted from ChEMBL 23* according to the following rules:

  1. The target must have a type of 'SINGLE PROTEIN', 'PROTEIN COMPLEX', or 'PROTEIN COMPLEX GROUP'
  2. Affinity types are combined and normalised as follows:
    Kd = Dissociation constant, Kd, K app, K Bind, K calc, Kd', KD app, KD', Kd(app), KD50, Kdiss, Relative Kd, Binding constant, K aff, K diss, KD/Ki
    pKd = -Log Kdiss, -Log KD50, pKd, pKD, logKd, -Log Kd, Log Kd, -Log KD, Log KD
    Ki = Adjusted Ki, Ki, ki, Ki app (inact), Ki app, Ki(app), Ki_app, Ki', Ki'', KI', K'i, Kiact, Ki high, Ki low, KiH, KiL, Kii, KII, Kic, Ki.c, Ki comp, Ki' uncomp
    pKi = pKi(app), pKi, -Log K0.5, Log Ki, logKi, -Log Ki, pKiH, pKiL
    IC50 = IC50 app, IC50, IC50 max, I50, Mean IC50, IC50H, IC50L
    pIC50 = pIC50, pIC50(app), -Log I50, logIC50, log IC50, Log IC50, -Log IC50, pI50, pIC50(calc)
    EC50 = EC50
    pEC50 = pEC50 diss, pEC50, -Log EC50, Log EC50, logEC50
    A2 = A2
    pA2 = pA2, pA2(app), pA2 app, pA2/pKB
  3. Raw data (e.g. Kis are converted into their negative log to base 10 values (e.g. pKis)
  4. Activities deemed by ChEMBL curators to be "outside typical range" are ignored (to prevent skew)
  5. Only binding ('B') and functional ('F') assays are included (no large-scale screening data)

Tables of activity data - Below the charts are tables listing all the data points included in the dataset. These are divided up by target and species and the source database is indicated, with assay description if available. The GtoPdb standard data type (pKd, pKi, pIC50, pEC50 or pA2) and value are given alongside the source database's original value and type (which may be the original data reported in the publication or that has been further curated by the ChEMBL team using one of the activity types given above). We recommend always checking the data in the original reference, which is provided along with a PubMed link.

*For more information about ChEMBL see their publication:

A.P. Bento, A. Gaulton, A. Hersey, et al. (2014). The ChEMBL bioactivity database: an update. Nucl. Acids Res. Database Issue. 42 D1083-D1090. [PMID:24214965]

Ligand List

The Guide to PHARMACOLOGY ligand list provides a directory of ligands described in the database, divided into subsets according to chemical category. A list of approved drugs and a list of ligands labelled with a chemical group, such as a radioactive isotope, are also provided. Ligands are sorted alphabetically as far as possible.

Glossary

Ligand actions
Agonist/full agonist A ligand that binds to a receptor and alters the receptor state resulting in a biological response. Conventional agonists stabilise an active conformation of a receptor and increase receptor activity. When the receptor stimulus induced by an agonist reaches the maximal response capability of the system (tissue), then it will produce the system maximal response and be a full agonist in that system
Inverse agonist A ligand that by binding to unoccupied receptors reduces the fraction of them in an active conformation. For nuclear receptors, an inverse agonist refers to ligands that can promote co-repressor recruitment
Partial agonist Agonists that in a given tissue, under specific conditions, cannot elicit as large an effect (even when applied at high concentration, so that all the receptors should be occupied) as can another agonist acting through the same receptors in the same tissue
Activator Ligands that activate ion channels by binding directly to them, including ligands that cause a change in the voltage dependence of channel gating that favours activation
Antagonist An antagonist is a drug that reduces the action of another drug, generally an agonist
Channel blocker Ligands that block ion movement through ion channels
Inhibitor Ligands that inhibit ion channel gating by directly binding to the channels, including ligands that inhibit ion channel activation and those that inhibit ion channel inactivation
Allosteric regulator A ligand that increases (positive) or decreases (negative) the action of an agonist or antagonist by combining with a distinct site on the receptor macromolecule. Neutral allosteric ligands bind to an allosteric site without affecting the binding or function of orthosteric ligands but can still block the action of other allosteric modulators that act via the same allosteric site
Orthosteric ligand Ligands that act by binding to the same site as does the physiological agonist of the receptor
Potentiation Refers to the enhancing effect of an allosteric regulator acting at an ion channel
Inhibition Refers to the inhibiting effect of an allosteric regulator acting at an ion channel
Selectivity Where a ligand type is selective for a given receptor or ion channel subunit, this is specifically indicated
Site of action In certain ion channels, the particular subunit to which the ligand binds is specified
Context In certain cases, the ligand context (intracellular, luminal, cytosolic or extracellular) is specified
Ligand classifications
Approved All ligands in the database which are currently, or have been in the past, approved for human clinical use by a regulatory agency
Synthetic organics Low molecular weight, non-polymeric compounds produced via either total synthesis or semi-synthetic processes
Metabolites Low molecular weight, non-peptidic, biogenic compounds produced by life processes (normally endogenous and of animal origin, including hormones and neurotransmitters) and their close analogues
Natural products Non-peptidic, biogenic compounds derived from living organisms and their close synthetic derivatives
Endogenous peptides Peptides encoded in the human, rat and mouse genomes
Other peptides Synthetic, semi-synthetic and natural peptides encoded in genomes other than human, rat and mouse (including oligopeptides and cyclic peptides)
Inorganics Ions and other inorganic compounds
Antibodies Including therapeutic monoclonal antibodies.
Probes/labelled ligands A ligand that allows quantitative pharmacological data to be derived from its interactions with a binding partner, usually through the use of biophysical methods. Thus, the majority of these probes are "radiolabelled" or tagged with unstable isotopes, conventionally with 3H-, 14C-, 125I- or 35S-. More recently, PET (Positron Emission Tomography) makes use of 11C- or 18F-labelled ligands, which are also unstable atoms. SPECT (Single Photon Emission Computed Tomography) often employs a metastable isotope 99mTc-. These radiolabelled ligands are sometimes referred to as radioligands. The use of stable isotope forms of ligands is currently more common in metabolic studies. Alternatively, probes can be labelled by fluorescent tags or small chemical entities, such as biotin.
Ligand structural information and properties
SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings
Canonical SMILES SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications
Isomeric SMILES SMILES include chiral and isotopic specification
InChI standard identifier (IUPAC International Chemical Identifier) InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching
InChI standard key An InChIKey is a simplified version of a full InChI, designed for easier web searching
Calculated Physico-chemical Properties Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK Toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand.
Receptor information
Nomenclature The recommended nomenclature for a structurally and operationally distinct target in a given family. Where this is the NC-IUPHAR published recommended nomenclature, this is specified in the Overview section with references to the relevant articles in Pharmacological Reviews. In cases where there are no published NC-IUPHAR recommendations, the adopted nomenclature is usually one of: the HGNC approved gene name, a name commonly used in the literature or a preliminary recommendation from NC-IUPHAR.
Principal transduction Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK Toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand.
Functional Characteristics Provides details of the conductance, voltage-dependence, rectification and selectivity properties of ion channels
Hs, Mm, Rn Indicates the species of the target. Hs: Homo sapiens; Mm: Mus musculus; Rn: Rattus norvegicus
Experimental measures of ligand action
EC50 The molar concentration of an agonist that produces 50% of the maximal possible effect of that agonist. Other percentage values (EC20, EC40, etc.) can be specified. The action of the agonist may be stimulatory or inhibitory
IC50 This term is used in a number of ways: (i) the molar concentration of an antagonist that reduces the response to an agonist by 50%; the concentration of agonist should be given; (ii) the molar concentration of an unlabeled agonist or antagonist that inhibits the binding of a radioligand by 50%; the concentration of radioligand should be given; (iii) the molar concentration of an inhibitory agonist that reduces a response by 50% of the maximal inhibition that can be attained; this latter usage is not recommended-instead the term, EC50, should be used since this is an agonist effect
KB KB refers to the equilibrium dissociation constant of a ligand (traditionally, a competitive antagonist) determined by means of a functional assay
Kd Kd refers to the equilibrium dissociation constant of a ligand determined directly in a binding assay using a labeled form of the ligand
Ki Ki refers to the equilibrium dissociation constant of a ligand determined in inhibition studies. The Ki for a given ligand is typically (but not necessarily) determined in a competitive radioligand binding study by measuring the inhibition of the binding of a reference radioligand by the competing ligand of interest under equilibrium conditions
Km The Michaelis constant (Km) defines the concentration of substrate at which the reaction rate is half of the maximum rate (Vmax) achieved by the system at maximum substrate concentrations.
pA2 pA2 The negative logarithm to base 10 of the molar concentration of an antagonist that makes it necessary to double the concentration of the agonist needed to elicit the original submaximal response obtained in the absence of antagonist
pEC50 The negative logarithm to base 10 of the EC50 of an agonist
pIC50 The negative logarithm to base 10 of the IC50 of an agonist or antagonist
pKB The negative logarithm to base 10 of the KB
pKd The negative logarithm to base 10 of the Kd
pKi The negative logarithm to base 10 of the Ki
pKm The negative logarithm to base 10 of the Km
Concentration range Where affinity data are not available, the concentration range of ligand used for the study is displayed (in M)
Rank order of potency The order of potency of the activity of a series of ligands at a particular target
Rank order of affinity The order of substrate binding strength for a particular enzyme

Database Links

Gene databases
Ensembl Provides a centralised resource for geneticists, molecular biologists and other researchers studying eukaryotic genomes. It is able to automatically generate graphical views of the alignment of genes and other genomic data against a reference genome.
Entrez Gene Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
GUDMAP With information supplied by a consortium of laboratories, the GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an online molecular atlas of gene expression for the developing organs of the genitourinary tract in mice, with access to primary data, high resolution molecular anatomy images, model mouse strains, and tutorials describing genitourinary tract organogenesis.
HGNC The authoritative source of approved human gene names and symbols. HGNC approves a unique and meaningful name for every known human gene based on a query of experts.
KEGG A database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem; includes information from large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
MGD Includes data on mouse gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
RGD Provides access to the most current, complete set of rat genomic and genetic data available, as well as the most innovative tools for analyzing this data.
RCSB PDB A repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. The data are typically obtained by X-ray crystallography or NMR spectroscopy.
RefSeq A database providing an annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products, with separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts.
UniProtKB A database of protein sequence and functional information, many of which are derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.
Pharmacology databases
BindingDB A public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
ChEMBL An online resource of bioactive drug-like small molecule structure-activity data, including 2-D structures, calculated properties and curated bioactivities from medicinal chemistry literature. Links are provided to ligand and target pages.
DrugBank A bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, pathway) information. Note that DrugBank is free for academic and non-profit use but commercial users require a license.
Chemistry databases
ChEBI A database and ontology of molecular entities focused on 'small' chemical compounds. These molecular entities are either products of nature or synthetic products used to intervene in the processes of living organisms. Molecules directly encoded by the genome, such as nucleic acids, proteins and peptides derived from proteins by proteolytic cleavage, are not as a rule included in ChEBI.
ChemSpider A chemical structure database providing fast access to over 25 million structures, properties and associated information. It is considered one of the primary chemistry internet portals and its mission includes improving the quality of public chemistry data sources through automated and crowd-sourced curation with expert review.
HMDB A database of small molecule metabolites found in the human body linked to chemical, clinical and molecular biology/biochemistry data.
PubChem A database of chemical molecules and their activities against biological assays.
Nature Lipidomics Gateway Information, tools and resources for researchers interested in lipid biology.
Disease/variant databases
dbSNP The NCBI Database for Short Genetic Variations (dbSNP) catalogues short variations in nucleotide sequences from a wide range of organisms.
OMIM A database that catalogues all the known human diseases with a genetic component, links them to the relevant genes, references and tools for genomic analysis.
Orphanet A resource providing an inventory, classification and encyclopaedia of rare diseases and their associated genes.
UniProtKB/Swiss-Prot Variant A summary of information related to variants and computed information such as the conservation of the modified residues across orthologous species.
Antibody databases
IMGT/mAb-DB A database of monoclonal antibodies (IG, mAb) and fusion proteins for immune applications (FPIA).
GPCR-specific databases
BitterDB A database of bitter compounds obtained from the literature and from Merck index and their associated human bitter taste receptors (hT2Rs).
GPCRDB An information system for GPCRs containing data on sequences, ligand binding constants and mutations along with tools to aid in visualisation and data analysis.
Nuclear receptor-specific databases
NURSA The Nuclear Receptor Signaling Atlas is a resource for validated information on nuclear receptor signalling, structure, function and role in disease.
Enzyme-specific databases
BRENDA A resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalysed biochemical reaction.
KEGG BRITE A collection of hierarchical classifications representing various aspects of biological systems.
MEROPS The MEROPS database provides access to information on peptidases (or proteases) and the proteins and small molecules that inhibit them, presented in a hierarchical, structure-based classification system.
General databases
PubMed References in Guide to PHARMACOLOGY are directly linked to citations in PubMed using PubMed IDs.
Wikipedia Although not always authoritative, it often provides lay, easily-digestible information on drugs and drug targets.