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 1,039,234 binding data, for 6,795 protein targets and 442,444 small molecules.

There are 2312 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 5782 crystal structures allowing proteins to 85% sequence identity.

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  1. We are pleased to announce BindingDB's new Advanced Search tool, which may be accessed with the link shown above. Please feel free to contact us with your comments and suggestions!
Journal Curation
by BindingDB
BindingDB continually curates a set of journals not covered by other public databases. As of February 2014, the status of our current curation effort is as follows:
  1. ACS Chemical Biology 2006-2014 (vol 1-9) magnifying glass
  2. ACS BioChemistry 1962-2013 (vol 1-52) magnifying glass
  3. Bioorganic Chemistry 1971-2013 (vol 1-47) magnifying glass
  4. BMC Chemical Biology 2001-2012 (vol 1-12) magnifying glass
  5. ChemBioChem 2000-2013 (vol 1-14) magnifying glass
  6. Chemical Biology & Drug Design 2006-2013 (vol 67-81) magnifying glass
  7. Chemistry & Biology 1994-2013 (vol 1-20) magnifying glass
  8. Journal of Biological Chemistry 1989-2013 (vol 264-288) magnifying glass
  9. Journal of Chemical Biology 2008-2013 (vol 1-6) magnifying glass
  10. Journal of Enzyme Inhibition and Medicinal Chemistry 1997-2009 (vol 11-24) magnifying glass
  11. Nature Chemical Biology 2005-2013 (vol 1-9) magnifying glass
  12. Medicinal Chemistry Research 2004-2010 (vol 13-19) magnifying glass
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BindingDB News

November 2013. Approximately 750 new protein-ligand validation sets have been automatically generated. Each dataset is a congeneric series with at least one associated protein-ligand co-crystal structure..

November 2013. We have used automated procedures to dock many compounds for which no co-crystal structures are available, using the existing co-crystal structures as models. The results are integrated with the rest of BindingDB, including the validation sets; or you can review the whole set of dockings here.

September 2013. BindingDB is now curating US patents. The patent data are available here, and are also accessible through our regular searching and browsing pages.

September 2013. Try the new SCOP browser to search for proteins by specific fold.

June 2013. Try the new AffyNet tool for visualization networks of Ligand-Target binding affinities. Links are provided below each Target and Ligand in the Results tables. This tool is still developmental, and we would appreciate comments and suggestions.

March 2013. A new pathway browser allows for retrieving data grouped by pre-sorted Reactome pathways.

March 2013. A new Web Services tab describes the BindingDB API, and provides KNIME workflows for easy retrieval of data.