The Protein Data Bank (PDB) was established in 1971 with just seven X-ray crystallographic structures of proteins as the first open access digital resource in the biological sciences. As of November 2015, the PDB global archive holds more than 113,000 experimentally determined 3D structural models of biological macromolecules. Some 76% of these intries include at least one non-polymeric small molecule ligand. Small-molecule ligands/drugs found in PDB entries are described in detail in the PDB Chemical Component Dictionary (CCD), which utilizes the data representation for chemical components developed for the Macromolecular Crystallographic Information Framework data dictionary. Each chemical definition in the CCD includes descriptions of chemical properties, such as stereochemical assignments, chemical descriptors, and systematic chemical names. A set of atomic model coordinates from a selected experimental entry and a computed set of ideal atomic coordinates are provided for each entry in the CCD.<br/> <br/>Every structure deposited to the PDB undergoes an extensive validation process, which was developed in consultation with the scientific community by the Worldwide Protein Data Bank organization (wwdpb.org) that is responsible for managing the PDB archive. During and structure determination and refinement, experimentalists are encouraged to access the anonymous wwPDB Validation Server (http://wwpdb-validation.wwpdb.org/) to validate their structures prior to deposition. For ligands, the wwPDB Validation Report includes both geometrical and model fit diagnostic information. The outcome of a recent wwPDB/CCDC/D3R Ligand Validation Workshop hosted by the RCSB Protein Data Bank in July 2015 will described, together with plans to implement recommendations therefrom.<br/>

Small-molecule ligand/drug representation and validation in the Protein Data Bank

251st National Meeting (2016)

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