The RCSB Protein Data Bank (RCSB PDB; rcsb.org) provides access to the PDB archive––the single worldwide repository for three-dimensional, experimentally determined protein and nucleic acid-containing structures. It houses over 120,000 biomolecules with about 21,000 unique bound ligands. Recently, there has been a significant increase in the number of entries that include ligands. Currently, ligand entries in the PDB provide only basic identification information on their web pages, e.g., molecular formula or InChI string as well as limited DrugBank information. To enrich the information represented on web pages of ligand entries and provide direct access to relevant compound data to users, we compiled data information from external scientific resources using Stereo-SMILES search inputs––validated by InChIKey––from the PDB chemical component dictionary. We produced a data structure, an external reference file (ERF), of enriched ligand definitions that holds information for 8 additional categories. This data structure has been used to map the data onto the web pages for ligand entries in order to provide improved searching and reporting protocols for users. In addition, the complementary data add considerable value for scientist and investigators using the PDB web resource, especially with regard to the biological role, relevance to disease, and biochemical properties of the ligands.

Enrichment of small molecule representation in the RCSB protein data bank

254th National Meeting (2017)

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