BindingDB is a publicly accessible database that contains approximately 20,000 experimentally determined binding affinities of protein–ligand complexes for 110 protein targets, including isoforms and mutational variants, and around 11,000 small molecule ligands. The data are extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets with structural data available in the Protein Data Bank (PDB). The BindingDB website supports various query types, including searches by chemical structure, substructure, similarity, protein sequence, ligand and protein names, affinity ranges, and molecular weight. Users can download data sets in annotated SDFiles for further analysis or use them for virtual screening of compound databases uploaded by the user. The data in BindingDB are linked to structural data in the PDB and the literature in PubMed. The database aims to accelerate the discovery of targeted ligands by providing functionalities that are not available in scientific journals, such as numerical data access, chemical structure queries, and large dataset downloads. Potential applications include analyzing ligands for specific targets to identify chemical features or pharmacophores that correlate with affinity. The database is freely accessible at http://www.bindingdb.org and can be accessed through links from compounds at PubChem.BindingDB is a publicly accessible database that contains approximately 20,000 experimentally determined binding affinities of protein–ligand complexes for 110 protein targets, including isoforms and mutational variants, and around 11,000 small molecule ligands. The data are extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets with structural data available in the Protein Data Bank (PDB). The BindingDB website supports various query types, including searches by chemical structure, substructure, similarity, protein sequence, ligand and protein names, affinity ranges, and molecular weight. Users can download data sets in annotated SDFiles for further analysis or use them for virtual screening of compound databases uploaded by the user. The data in BindingDB are linked to structural data in the PDB and the literature in PubMed. The database aims to accelerate the discovery of targeted ligands by providing functionalities that are not available in scientific journals, such as numerical data access, chemical structure queries, and large dataset downloads. Potential applications include analyzing ligands for specific targets to identify chemical features or pharmacophores that correlate with affinity. The database is freely accessible at http://www.bindingdb.org and can be accessed through links from compounds at PubChem.