Chemistry and drugs · Database
BindingDB
A public database of experimentally measured binding affinities between proteins and drug-like small molecules.
What BindingDB is
BindingDB is a public database containing experimentally measured binding affinities, focusing primarily on interactions between small, drug-like molecules and proteins considered candidate drug targets. Led by Michael Gilson at the UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences with NIH grant support, it also contains a small collection of host–guest binding data relevant to supramolecular chemistry.
The resource was conceived in the mid-1990s to overcome the fragmentation of quantitative affinity data across published journals. It aims to support medicinal chemistry and drug discovery, including the development of structure-activity relationships (SAR and QSAR), chemical biology, chemical genomics, and fundamental investigations into the physical chemistry of molecular recognition.
Computational researchers also rely on the collection to validate molecular modelling and computational chemistry workflows, such as molecular docking, scoring functions, and free energy calculation methods.
How it is organised
BindingDB aggregates quantitative affinity data derived from multiple experimental techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry (ITC), nuclear magnetic resonance (NMR), and radioligand or competition assays.
Because relying on community depositions proved insufficient, the project extracts records directly from the scientific literature, alongside selected PubChem confirmatory bioassays and entries from ChEMBL that specify a well-defined protein target. Curation prioritises small-molecule binding with drug-target proteins that have a three-dimensional structure deposited in the Protein Data Bank (PDB) or that can be accurately modelled based on a related protein structure.
Key facts
- Records
- 2.9M measurements
- Historical data size (March 2011)
- About 650,000 binding data points, 5,700 protein targets, and 280,000 small molecules
- Project lead
- Michael Gilson
- Host institution
- UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences
- Primary funding
- NIH (with initial development supported by NSF and NIST)
- Data sources
- Scientific literature extraction, selected PubChem confirmatory BioAssays, and ChEMBL protein-target entries
What you can use it for
- Structure-Activity Relationship (SAR) Analysis
- Medicinal chemists can survey binding data across chemical series to develop SAR and QSAR models for drug discovery.
- Validation of Molecular Docking and Scoring
- Computational chemists can benchmark docking algorithms, scoring functions, and free energy prediction methods against experimental affinity measurements.
- Chemical Biology and Target Profiling
- Researchers can query protein targets or chemical structures to explore small-molecule interactions across biological targets.
- Supramolecular Host–Guest Studies
- Physical and supramolecular chemists can inspect non-covalent binding data gathered for host–guest model systems.
Query it here
The research agent queries BindingDB directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Combines data from literature curation, PubChem confirmatory BioAssays, and ChEMBL into a single queryable resource.
- Web interface supports flexible chemical searching via substructure and chemical similarity queries as well as protein target browsing.
- Captures quantitative affinity values from diverse biophysical techniques, including ITC, NMR, enzyme kinetics, and radioligand assays.
Watch out for
- Data curation concentrates predominantly on drug-target proteins with structures in the PDB or reliable homology models, rather than broad proteome-wide coverage.
- Relies primarily on project-driven literature curation and external database imports because direct community depositions remain limited.
Questions
Can I search BindingDB without writing code?
Yes. The research agent queries BindingDB directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from BindingDB?
BindingDB-curated data CC BY 3.0; ChEMBL-imported rows CC BY-SA 3.0. Terms: https://www.bindingdb.org/rwd/bind/info.jsp
What types of binding affinity measurements are included?
BindingDB records data from various assay types, including enzyme inhibition and kinetics, isothermal titration calorimetry (ITC), NMR, and radioligand or competition assays.
How can I search and retrieve data from BindingDB?
The web interface provides tools to browse by protein target name or journal citation, query by chemical similarity and substructure, and download results by target or query output.
Does BindingDB include interactions other than protein–ligand binding?
While the primary focus is small-molecule interactions with protein drug targets, it also holds a small collection of host–guest binding data for supramolecular systems, alongside historical data covering protein–protein interactions.
Written from BindingDB's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.