The relevance of the Cambridge Structural Database in protein crystallography

Abstract

The importance of high-resolution crystal structure data of small molecules to protein crystallography is highlighted. Specific areas covered include: mean molecular dimensions for peptidic fragments and other biologically important substructures, conformational information, hydrogen-bond geometries and their directionality, and other strong non-covalent interactions. The value of the IsoStar knowledge base of intermolecular interactions, derived from the CSD and from protein–ligand complexes in the PDB, is illustrated. The value of structural information from small molecules to our understanding of protein–ligand binding is also discussed, together with examples of how this information is important in the prediction of ligand binding modes and in software tools for protein–ligand docking. Keywords: Cambridge Structural Database; databases; hydrogen bonding; intermolecular interactions; IsoStar; metal coordination geometry; nonbonded interactions; Protein Data Bank; protein–ligand interactions; structure validation; van der Waals radii