BindingDB Measured Affinity Database

Public web-accessible repository of experimentally measured protein–small-molecule binding affinities (Ki, Kd, IC50, ΔG, ΔH).

Specifications & Metrics

type: Quantitative Protein–Ligand Affinity
maintainer: Michael K. Gilson laboratory at the Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego
identifier format: BDBM<integer> monomer IDs linked to UniProt targets and PubChem CIDs
license: Creative Commons Attribution 3.0 / Public Domain data downloads
introduced: 2000

Conceived in the mid-1990s and validated at a September 1997 NIST-sponsored workshop with NSF and NIST support, BindingDB compiles quantitative experimental binding data for candidate drug-target proteins and small drug-like ligands.
BindingDB records affinities measured by enzyme inhibition kinetics, isothermal titration calorimetry (ITC), surface plasmon resonance, NMR, and radioligand competition, alongside assay pH, temperature, and buffer conditions.
In addition to literature curation and patent extraction from U.S. chemical patents, BindingDB includes supramolecular host–guest binding constants used to benchmark molecular docking scoring functions and free-energy force fields.