Evaluation of the Complementarity of Three Major Databases of Protein–Ligand Binding Affinity Data

Public databases including ChEMBL, BindingDB, and PDBbind curate such data with distinct focuses, yet their data overlap and complementary attributes remain insufficiently quantified. In this work, we systematically cross-mapped protein–ligand binding data in PDBbind (version 2024) against data records sourced from ChEMBL (version 35) and BindingDB (version 2025.08).

Our analysis revealed that merely 22.1% and 23.9% of PDBbind’s annotated protein–ligand complexes possess matching binding data records in ChEMBL and BindingDB, respectively, confirming that the PDBbind dataset is not a subset of the other two larger repositories. This limited overlap arises from fundamental differences in scope: ChEMBL and BindingDB center on drug discovery datasets, whereas the data entries in PDBbind encompass a broader chemical and biological landscape.