1 sc-PDB: a database for identifying variations and multiplicity of “druggable ” binding sites in proteins

Background: The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8 166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classifica-tion of all the binding sites within a functional class. Method: The sc-PDB entries were first clustered according to the protein name indifferently of species. For each cluster, we identified dissimilar sites (e.g., catalytic and allosteric sites of an enzyme). Scope and applications: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In struc-ture-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and/or structure). Availibility: The sc-PDB database is freely available at