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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 1,252,088 binding data, for 6,468 protein targets and 552,906 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 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)
  2. 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. (May 2016)
  3. 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)
Patent Curation
by BindingDB

BindingDB curates US Patents with protein-small molecule binding data. As of September 2016, 1229 patents have been processed.

Journal Curation
by BindingDB
BindingDB continually curates a set of journals not covered by other public databases. As of September 2016, the status of our current curation effort is as follows:
  1. ACS Chemical Biology 2006-2016 (vol 1-11) magnifying glass
  2. ACS BioChemistry 1965-2016 (vol 4-55) magnifying glass
  3. Bioorganic Chemistry 1990-2016 (vol 18-68) magnifying glass
  4. BMC Chemical Biology 2001-2010 (vol 1-10) magnifying glass
  5. ChemBioChem 2001-2016 (vol 2-17) magnifying glass
  6. Chemical Biology & Drug Design 2006-2016 (vol 67-88) magnifying glass
  7. Chemistry & Biology 1995-2015 (vol 2-22) magnifying glass
  8. Journal of Biological Chemistry 1982-2013 (vol 257-288) magnifying glass
  9. Journal of Chemical Biology 2010-2010 (vol 3-3) magnifying glass
  10. Journal of Enzyme Inhibition and Medicinal Chemistry 2002-2009 (vol 17-24) magnifying glass
  11. Nature Chemical Biology 2006-2015 (vol 1-11) magnifying glass
  12. Medicinal Chemistry Research 2004-2013 (vol 13-22) magnifying glass
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Video Tutorials
  1. Get all data from an article
  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

March 2016.BindingDB's Advanced Search now allows you to download your search results in Excel format.

December 2015.We are delighted to announce that Elsevier's Science Direct journals now include links from articles to BindingDB datasets, where available! For an example, go to this article, and see the "Data for this Article, BindingDB" link on the right.

September 2015. We plan to post the latest BindingDB user survey on or about October 5. We would greatly appreciate your feedback and suggestions! Note, however, that you are always free to click through the survey to the regular home-page.

September 2015. All compounds in BindingDB have now been assigned a BindingDB Molecule ID, such as BDBM50183711. (The numeric component is also known, internally, as a Monomer ID.)

September 2015. BindingDB should give you faster performance now, as we have upgraded the main server. Please let us know immediately if you notice any problems.

July 2015. Please try our new tool to map from one or more proteins of known sequence to known or potential ligands: Find Compounds for My Targets.

April 2015. BindingDB has improved security. We now use SSL to transmit passwords securely, and forgotten passwords are now handled with a reset link.

March 2015. The BindingDB results tables now provide links from protein targets to antibodies in Antibodypedia, and from ligands to UniChem.