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BindingDB is 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. BindingDB contains 1,357,744 binding data, for 7,140 protein targets and 605,839 small molecules.

There are 2291 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 5816 crystal structures allowing proteins to 85% sequence identity.

Simple Search
Article Titles, Authors, Assays, Compound Names, Target Names

Use ? for single-letter wild-card or * for general wild-card.
For example, "adeny*" or "adeny?". Query cannot start with wild card.
Advanced Search Combine multiple search criteria, such as chemical structures, target names, and numerical affinities; restrict searches by data source, such as BindingDB, ChEMBL, PubChem, and Patents.
Messages
  1. We are pleased to report that the NIH has renewed its support for BindingDB. Thanks to all who filled out our survey and provided supporting messages! (June 2017)
  2. Drug Design Data Resource (D3R) datasets have been integrated into BindingDB and are also available here: https://www.bindingdb.org/bind/ByD3R.jsp (June 2017)
Patent Curation
by BindingDB

BindingDB curates US Patents with protein-small molecule binding data. As of July 2017, BindingDB's patent dataset comprises:

  1. Patents: 1,639
  2. Binding measurements: 173,275
  3. Compounds: 116,165
  4. Target proteins: 1,066
  5. Assays: 2,273
Journal Curation
by BindingDB
BindingDB continually curates a set of journals not covered by other public databases. As of July 2017, the status of our current curation effort is as follows:
  1. ACS Chemical Biology 2006-2017 (vol 1-12) magnifying glass
  2. ACS BioChemistry 1965-2017 (vol 4-56) magnifying glass
  3. Bioorganic Chemistry 1990-2017 (vol 18-73) magnifying glass
  4. BMC Chemical Biology 2001-2010 (vol 1-10) magnifying glass
  5. ChemBioChem 2001-2017 (vol 2-18) magnifying glass
  6. Chemical Biology & Drug Design 2006-2017 (vol 67-89) magnifying glass
  7. Chemistry & Biology 1995-2015 (vol 2-22) magnifying glass
  8. Journal of Biological Chemistry 1982-2014 (vol 257-289) magnifying glass
  9. Journal of Chemical Biology 2010-2010 (vol 3-3) magnifying glass
  10. Journal of Enzyme Inhibition and Medicinal Chemistry 2002-2011 (vol 17-26) magnifying glass
  11. Nature Chemical Biology 2006-2017 (vol 1-13) magnifying glass
  12. Medicinal Chemistry Research 2004-2013 (vol 13-22) magnifying glass
  1. PubMed IDs: 3,280
  2. Binding measurements: 107,259
  3. Compounds: 44,406
  4. Target proteins: 3,113
  5. Assays: 4,764
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  2. Download all data for a target of interest
  3. Find and view all data for a target of interest
  4. Find my compound's targets
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BindingDB News

September 2016. BindingDB's Advanced Search results now include a new "Diseases" tab, with information about the probable disease-relatedness of the Targets found in your search. This information is drawn from the source Articles and structured based on Disease Ontology. Please give it a try and let us know what you think of it!

May 2016. We have added a new Webservice, getLigandsByUniprots, which accepts list of UniProt IDs and returns all ligands for the proteins in the list that bind better than a user-specified threshold. A switch allows selection of results for all ligands, only ligands identified as commercially available, or only ligands identified as FDA-approved drugs. Another switch allows the default XML format to be replaced by JSON.

May 2016. The Target Names page has a new column, Commercially Available Compounds, which provides links only to BindingDB data for commercially available compounds. To buy a compound, follow the "Purchase" link under "Ligand Links" in pages like this.

May 2016. BindingDB is collaborating with the NDEx project to support annotation of biomolecular networks with small molecule binding data. This page provides further details, and you can view BindingDB as NDEx networks here. The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate and publish biological network knowledge.