Overview

As a new feature we are pleased to announce the first version of our REST web services for beta testing. Currently the web services serve up JSON files, though we will look at extending the range of options in the future. You can retrieve families, targets, genes, ligands and text annotations.

The GtoPdb web service base URL (base_url) is http://www.guidetopharmacology.org/services/ and points to the current version of the web services API. The API will be updated in accordance with normal database release cycles to accommodate new data types as required.

Specific services may be accessed by appending the correct portion of the URL as given below in the tables. Optional parameters can be included by appending a question mark (?) to the end of the service name and separating parameters with ampersand (&), e.g. http://www.guidetopharmacology.org/services/targets/290/interactions?affinityType=pKi&species=Human

The Guide to PHARMACOLOGY database is licensed under the Open Data Commons Open Database License (ODbL) and its contents are licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported license.

Further information may be obtained by emailing us.

Target web services

ServiceURLParameters
List of targets{base_url}/targets
type (optional): The target class abbreviation, i.e. 'GPCR', 'NHR', 'LGIC', 'VGIC', 'OtherIC', 'Enzyme', 'CatalyticReceptor', 'Transporter', 'OtherProtein', 'AccessoryProtein'
name (optional): search for targets by name
geneSymbol (optional): a human, mouse or rat gene symbol
ecNumber (optional): an Enzyme Commission (EC) number
accession (optional): an external database accession number or Id
database (optional): the name* of the database the accession number relates to (default = UniProt)
Single target{base_url}/targets/{targetId}
targetId: a GtoPdb target Id
List of families{base_url}/targets/families
type (optional): target class abbreviation as above
name (optional): search for families by name
Single family{base_url}/targets/families/{familyId}
familyId: a GtoPdb family Id
Component subunits{base_url}/targets/{targetId}/subunits
Complexes{base_url}/targets/{targetId}/complexes
Synonyms{base_url}/targets/{targetId}/synonyms
Gene and protein information{base_url}/targets/{targetId}/geneProteinInformation
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Database links{base_url}/targets/{targetId}/databaseLinks
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
database (optional): the name* of the database to retrieve links for
Natural/endogenous ligands{base_url}/targets/{targetId}/naturalLigands
Interactions{base_url}/targets/{targetId}/interactions
type (optional): the type of interaction, i.e. 'Activator', 'Agonist', 'Allosteric modulator', 'Antagonist', 'Antibody', 'Channel blocker', 'Gating inhibitor', 'Inhibitor', 'Subunit-specific'
affinityType (optional): one of 'pA2', 'pEC50', 'pIC50', 'pKB', 'pKd', 'pKi'
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
affinity (optional): returned results must have affinity greater than this value, e.g. 7.5.
Rank order lists of ligands and other activators{base_url}/targets/{targetId}/rankOrder
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Function{base_url}/targets/{targetId}/function
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Tissue distribution{base_url}/targets/{targetId}/tissueDistribution
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Functional assay{base_url}/targets/{targetId}/functionalAssay
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Gene expression and pathophysiology{base_url}/targets/{targetId}/geneExpressionPathophysiology
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Physiological consequences of altering gene expression{base_url}/targets/{targetId}/alteredExpression
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Xenobiotics influencing gene expression{base_url}/targets/{targetId}/xenobioticsGeneExpression
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Clinically-relevant mutations and pathophysiology{base_url}/targets/{targetId}/pathophysiology
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Variants{base_url}/targets/{targetId}/variants
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
PDB structures{base_url}/targets/{targetId}/pdbStructure
Associated proteins{base_url}/targets/{targetId}/associatedProteins
Ion selectivity{base_url}/targets/{targetId}/ionSelectivity
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Ion conductance{base_url}/targets/{targetId}/ionConductance
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Ion channel voltage dependence{base_url}/targets/{targetId}/voltageDependence
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
GPCR transduction mechanisms{base_url}/targets/{targetId}/transduction
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
NHR binding partners{base_url}/targets/{targetId}/bindingPartners
NHR co-regulators{base_url}/targets/{targetId}/coregulators
NHR target genes{base_url}/targets/{targetId}/targetGenes
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
NHR DNA binding sequence{base_url}/targets/{targetId}/dnaBinding
Enzyme reaction{base_url}/targets/{targetId}/reactions
Substrates{base_url}/targets/{targetId}/substrates
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Products{base_url}/targets/{targetId}/products
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Cofactors{base_url}/targets/{targetId}/cofactors
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Target comments{base_url}/targets/{targetId}/comments
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
database (optional): the name* of the database to retrieve links for
Target contributing authors{base_url}/targets/{targetId}/contributors
Family contributing authors{base_url}/targets/families/{familyId}/contributors
Family NC-IUPHAR subcommittee{base_url}/targets/families/{familyId}/subcommittee
Family overview{base_url}/targets/families/{familyId}/overview
Family comments{base_url}/targets/families/{familyId}/comments
Family introduction{base_url}/targets/families/{familyId}/introduction
Introduction contributing authors{base_url}/targets/families/{familyId}/introduction/contributors

Ligand web services

ServiceURLParameters
List of ligands{base_url}/ligands
type (optional): The ligand type, one of 'Synthetic organic', 'Metabolite', 'Natural product', 'Endogenous peptide', 'Peptide', 'Antibody', 'Inorganic', 'Approved', 'Withdrawn', 'Labelled', 'INN'
name (optional): search for ligands by name
geneSymbol (optional): a human, mouse or rat gene symbol
accession (optional): an external database accession number or Id
database (optional): the name* of the database the accession number relates to (default = PubChemCID)
inchikey (optional): the ligand's InChIKey, or for backbone matches (other isomers) just provide the backbone part (the first 14 characters)
lipinskyGt & lipinskyLt (optional): lower and upper cut-offs for the number of Lipinsky's rules broken
logpGt & logpLt (optional): lower and upper cut-offs for the LogP
molWeightGt & molWeightLt (optional): lower and upper cut-offs for the molecular weight
hBondAcceptorsGt & hBondAcceptorsLt (optional): lower and upper cut-offs for the number of hydrogen bond acceptors
hBondDonorsGt & hBondDonorsLt (optional): lower and upper cut-offs for the number of hydrogen bond donors
rotatableBondsGt & rotatableBondsLt (optional): lower and upper cut-offs for the number of rotatable bonds
tpsaGt & tpsaLt (optional): lower and upper cut-offs for the topological polar surface area
Exact match structure search{base_url}/ligands/exact
smiles: a SMILES string to search
Substructure search{base_url}/ligands/substructure
smiles: a SMILES string to search
lipinskyGt & lipinskyLt (optional): lower and upper cut-offs for the number of Lipinsky's rules broken
logpGt & logpLt (optional): lower and upper cut-offs for the LogP
molWeightGt & molWeightLt (optional): lower and upper cut-offs for the molecular weight
hBondAcceptorsGt & hBondAcceptorsLt (optional): lower and upper cut-offs for the number of hydrogen bond acceptors
hBondDonorsGt & hBondDonorsLt (optional): lower and upper cut-offs for the number of hydrogen bond donors
rotatableBondsGt & rotatableBondsLt (optional): lower and upper cut-offs for the number of rotatable bonds
tpsaGt & tpsaLt (optional): lower and upper cut-offs for the topological polar surface area
Structure similarity search{base_url}/ligands/similarity
smiles: a SMILES string to search
similarityGt (optional): lower cut-off for the % similarity (default = 85)
lipinskyGt & lipinskyLt (optional): lower and upper cut-offs for the number of Lipinsky's rules broken
logpGt & logpLt (optional): lower and upper cut-offs for the LogP
molWeightGt & molWeightLt (optional): lower and upper cut-offs for the molecular weight
hBondAcceptorsGt & hBondAcceptorsLt (optional): lower and upper cut-offs for the number of hydrogen bond acceptors
hBondDonorsGt & hBondDonorsLt (optional): lower and upper cut-offs for the number of hydrogen bond donors
rotatableBondsGt & rotatableBondsLt (optional): lower and upper cut-offs for the number of rotatable bonds
tpsaGt & tpsaLt (optional): lower and upper cut-offs for the topological polar surface area
Single ligand{base_url}/ligands/{ligandId}
ligandId: a GtoPdb ligand Id
Path to image file{base_url}/ligands/{ligandId}/image
Ligand structure{base_url}/ligands/{ligandId}/structure
Component subunits{base_url}/ligands/{ligandId}/subunits
Complexes{base_url}/ligands/{ligandId}/complexes
Precursors (endogenous peptides){base_url}/ligands/{ligandId}/precursors
Molecular properties (non-peptides){base_url}/ligands/{ligandId}/molecularProperties
Synonyms{base_url}/ligands/{ligandId}/synonyms
Database links{base_url}/ligands/{ligandId}/databaseLinks
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
database (optional): the name* of the database to retrieve links for
Interactions{base_url}/ligands/{ligandId}/interactions
type (optional): the type of interaction, i.e. 'Activator', 'Agonist', 'Allosteric modulator', 'Antagonist', 'Antibody', 'Channel blocker', 'Gating inhibitor', 'Inhibitor', 'Subunit-specific'
affinityType (optional): one of 'pA2', 'pEC50', 'pIC50', 'pKB', 'pKd', 'pKi'
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
affinity (optional): returned results must have affinity greater than this value, e.g. 7.5.
asTarget (optional): boolean which indicates if this ligand Id should be considered as the target of interactions by other ligands, e.g. antibodies (default = true)
asLigand (optional): boolean which indicates if this ligand Id should be considered as the ligand interacting with other targets (default = true)
Rank order lists of ligands at targets{base_url}/ligands/{ligandId}/rankOrder
species (optional): the species common name, e.g. 'Human, 'Mouse', 'Rat' etc.
Ligand comments and clinical use information{base_url}/ligands/{ligandId}/comments

Examples

These are a few example use cases for the web services.

  1. Retrieve the target with Ensembl gene Id ENSG00000097007:
    http://www.guidetopharmacology.org/services/targets?accession=ENSG00000097007&database=EnsemblGene
  2. Retrieve the target encoded by HGNC gene symbol CATSPER4:
    http://www.guidetopharmacology.org/services/targets?geneSymbol=CATSPER4
  3. Search for the target with name HER3:
    http://www.guidetopharmacology.org/services/targets?name=HER3
  4. Find the subunits of 5-HT3AB (target Id 378):
    http://www.guidetopharmacology.org/services/targets/378/subunits
  5. Find agonists of GPER (target Id 221) with pKi >= 7:
    http://www.guidetopharmacology.org/services/targets/221/interactions?type=Agonist&affinityType=pKi&affinity=7
  6. Retrieve all the approved drugs:
    http://www.guidetopharmacology.org/services/ligands?type=Approved
  7. Find synonyms for tamoxifen (ligand Id 1016) :
    http://www.guidetopharmacology.org/services/ligands/1016/synonyms
  8. Find ligands at least 80% similar to the structure CC(CN(C)C)CN1c2ccccc2Sc2ccccc12:
    http://www.guidetopharmacology.org/services/ligands/similarity?smiles=CC(CN(C)C)CN1c2ccccc2Sc2ccccc12&similarityGt=80
  9. Find ligands with the substructure Nc1cnc(Cl)c(N)n1 and calculated LogP between 0 and 2:
    http://www.guidetopharmacology.org/services/ligands/substructure?smiles=Nc1cnc(Cl)c(N)n1&logpGt=0&logpLt=2

Databases

* This is a list of the database names to use when searching for targets or ligands by accession number. For more information about these databases see the help page.

DatabaseDatabase name in GtoPdbTarget or ligand
BindingDB database of binding affinitiesBindingDBLigand
BitterDB database of bitter compoundsBitterDBTarget
BRENDA database of enzyme reactionsBRENDALigand
CAS Registry NumberCASLigand
Chemical Entities of Biological Interest (ChEBI)ChEBILigand
ChEMBL medicinal chemistry databaseChEMBLTarget & Ligand
NCBI Database for Short Genetic Variations (dbSNP)dbSNPTarget
DrugBankDrugBankTarget & Ligand
Ensembl GeneEnsemblGeneTarget & Ligand
Ensembl ProteinEnsemblProteinTarget
Ensembl TranscriptEnsemblTranscriptTarget
NCBI Entrez GeneEntrezGeneTarget & Ligand
GPCRDBGPCRDBTarget
Human Metabolome Database (HMDB)HMDBLigand
NCBI HomoloGeneHomoloGeneTarget
Human Protein Reference Database (HPRD)HPRDTarget
HGNC database of human gene namesHGNCTarget
IMGT/mAb-DB database of therapeutic monoclonal antibodiesIMGTLigand
LIPID MAPS Lipidomics GatewayLipidMapsLigand
MEROPS peptidase databaseMEROPSTarget
Mouse Genome InformaticsMGITarget
Nuclear Receptor Signaling AtlasNURSATarget & Ligand
Online Mendelian Inheritance in Man (OMIM)OMIMTarget & Ligand
Orphanet database of rare diseasesOrphanetTarget
NCBI Protein database GI numbersProteinGITarget & Ligand
Protein Data Bank (PDB)PDBLigand
Protein OntologyPROTarget
PubChem Compound Id (CID)PubChemCIDLigand
NCBI RefSeq NucleotideRefSeqNucleotideTarget & Ligand
NCBI RefSeq ProteinRefSeqProteinTarget & Ligand
Rat Genome DatabaseRGDTarget
NCBI UniGeneUniGeneTarget
NCBI UniGene Homo sapiensUniGeneHsTarget & Ligand
UniProtKB protein resourceUniProtTarget & Ligand
UniProtKB variant databaseUniProtVariantTarget

HTTP response codes

This is a listing of specific HTTP response error codes which can be returned by the GtoPdb web services and their meanings.

HTTP response codeMeaningDescription
204No contentAn empty page and a 204 no content response usually mean there are no results to display for the given URL (i.e. no data in the requested database table).
303See otherRedirection to an alternative location for the requested data (e.g. the path to a ligand image).
404Not foundEither a resource with that address or an entity such as a ligand with the given identifier cannot be found.