Contents

About IUPHAR-DB
Search Facility
Database Tables
GPCR Tables
Ion Channel Tables
Nuclear Receptor Tables
Enzyme Tables
Ligand Pages
Ligand List
Database Links

About IUPHAR-DB

IUPHAR-DB contributors
The IUPHAR database is developed under the auspices of NC-IUPHAR to provide an accurate educative resource to the scientific community. It relies on contributions by expert pharmacologists who volunteer their time. All contributors are attributed on the website, allowing receptor data pages to be properly cited.

Annotation procedure
NC-IUPHAR has a network of expert subcommittees (presently over 60), each responsible for developing the nomenclature for a receptor family and contributing data. Where no relevant subcommittee exists, data are captured by the curators or individual experts and peer reviewed by at least two external expert referees.

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

If you would like to get involved in reviewing, contributing to the data tables or just to make any comments please contact the curators: curators@iuphar-db.org.

Colour codes
Each family and receptor are given a colour code to indicate the status of their annotation in IUPHAR-DB:

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.

Search Facility

A quick text search box is provided in the left sidebar of all pages. Just enter keywords in the text field and press 'Search the database' to perform a matching text search on all data fields.

Advanced search tools can be accessed by following the links below the quick text search box on the left. Advanced search tools allow text searches on specific database fields, as well as non-text searches e.g. by accession number or chemical structure. Depending on the type of data you wish to search for you can choose between receptor search tools and chemical search tools.

Receptor and ligand searches now run across both IUPHAR-DB and our sister database, the Guide to Receptors and Channels (GRAC). Search results that match receptors in IUPHAR-DB will point to the IUPHAR-DB pages, from which there are links to the relevant GRAC database pages. Search results matching receptors which are only in GRAC point directly to the GRAC database. All ligand search results point to ligand pages on the IUPHAR-DB web site, which are provided in addition to identical pages on the GRAC database.

Receptor search tools

Ligand search tools

 

Database Tables (all targets)

Click here for an interactive PDF image of a receptor page (hover over red boxes to view descriptions).

Nomenclature [GPCRs and Ion Channels] - 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.

Nomenclature [Nuclear Hormone Receptors] - Typically the most commonly used name for the receptor.

Systematic Nomenclature [Nuclear Hormone Receptors] - 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.

Nomenclature [Enzymes and Catalytic Receptors] - 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) or is the HGNC approved name.

Abbreviated Name [Enzymes and Catalytic Receptors] - An abbreviated name commonly used in the literature.

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

Column Definition
Transmembrane domains (TM) The number of times the receptor 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 receptor protein.
Chromosomal location The genetic location of the receptor.
Gene symbol The official symbol given to the gene that codes for the receptor 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 receptor.
Reference A reference to the first paper(s) describing the cloning of the receptor.

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 several genomic databases (e.g. Ensembl, Entrez Gene, GeneCards), protein databases (e.g. RefSeq, Uniprot) and others such as ChEMBL (MedChem literature data on drug-like molecules and their targets) and PharmGKB (pharmacogenomics data). 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 receptor the unliganded, agonist, and antagonist bound structures where available. Links are provided to associate IUPHAR 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 receptor.
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.
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 receptors, structural information and links to similar ligands, where available.
Action This indicates how the ligand binds to the receptor (see the terms and symbols document for a definition of the terms).
Affinity A measure of how strongly the ligand binds to the receptor. 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 receptor (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).

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 Tables

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 Tables

Voltage-gated (VGIC) and ligand-gated (LGIC) ion channels

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 Tables

Receptor name - 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.

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.

 

Enzyme Tables

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) or is the HGNC approved name.

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

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 receptor is being studied, while synthetic inhibitors include drugs and other non-naturally occurring chemical agents.

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.

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.

 

Catalytic Receptor Tables

Nomenclature - The nomenclature used here is either the name 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) or the HGNC approved name.

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

E.C. Number - See above description for Enzymes.

 

Ligand Tables

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 Physical-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.

Classification - Compounds are assigned to the following general classes based on their origin and structural properties:

Synthetic compounds
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).
Inorganic compounds
Ions and other inorganic compounds.
Antibodies
Including therapeutic monoclonal antibodies.

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, PharmGKB, 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 receptors in the IUPHAR database, separated by receptor type (GPCR, ion channel, NHR, enzyme) and by species, and from the Guide to Receptors and Channels (GRAC). For full description see ligand table description above.

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

Screening Data - See above.

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.
Standard InChI (IUPAC International Chemical Identifier) and InChI Key
InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChI Key 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) - 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.

Please note that ligand pages are identical between IUPHAR-DB and our sister web site, the Guide to Pharmacology. All ligands can be searched and viewed on either web site.

 

Ligand List

The default view of the IUPHAR-DB ligand list includes only the ligands described in IUPHAR-DB. A complete list of ligands in both IUPHAR-DB and GRAC is available via the Guide to PHARMACOLOGY website and can be accessed via the link at the top of the page.

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.
GeneCards A searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes. Note that GeneCards is free for academic and non-profit use but commercial users require a license.
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.
HomoloGene An automated system for constructing putative homology groups from the genomes of a wide range of eukaryotic species.
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.
TreeFam A database of animal gene trees, encompassing inferred phylogenetic trees, predicted orthologues/parologues and the evolutionary history of genes.
UniGene A database of the transcriptome providing information on protein similarities, gene expression, cDNA clones, and genomic location.
Protein databases
HPRD An expert-curated database integrating domain structure, post-translational modification, interaction network and disease association information for all of the human proteome.
InterPro Integrates protein information from several allied databases into a single searchable resource providing protein family classification information, functional domain prediction and identification of other important sites on proteins.
PhosphoSitePlus An expert curated database providing access to information and tools useful to the study of in-vivo post-translational modification of proteins of the kinome.
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.
UniProt 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.
PharmGKB An integrated resource providing information on how variation in human genetics leads to variation in response to drugs.
iPHACE An integrative web-based tool to navigate in the pharmacological space defined by small molecule drugs contained in the IUPHAR-DB, with additional interactions present in PDSP. Extending beyond traditional querying and filtering tools, iPHACE offers a means to extract knowledge from the target profile of drugs as well as from the drug profile of protein targets.
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.
ZINC A database containing commercially available compounds for structure-based virtual screening.
Disease databases
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.
Nuclear receptor-specific databases
NURSA The Nuclear Receptor Signaling Atlas is a resource for validated information about 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.
ExplorEnz A resource providing access to the data of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature List, and which maintains the IUPAC standard formatting of chemical names.
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.

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