Tyzack JD, Fernando L, Ribeiro AJM, Borkakoti N, Thornton JM. Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.
Structure 2018;
26:565-571.e3. [PMID:
29551288 DOI:
10.1016/j.str.2018.02.009]
[Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/26/2018] [Accepted: 02/09/2018] [Indexed: 11/22/2022]
Abstract
There are numerous applications that use the structures of protein-ligand complexes from the PDB, such as 3D pharmacophore identification, virtual screening, and fragment-based drug design. The structures underlying these applications are potentially much more informative if they contain biologically relevant bound ligands, with high similarity to the cognate ligands. We present a study of ligand-enzyme complexes that compares the similarity of bound and cognate ligands, enabling the best matches to be identified. We calculate the molecular similarity scores using a method called PARITY (proportion of atoms residing in identical topology), which can conveniently be combined to give a similarity score for all cognate reactants or products in the reaction. Thus, we generate a rank-ordered list of related PDB structures, according to the biological similarity of the ligands bound in the structures.
We present PARITY, matching atoms in identical topology to gauge ligand similarity
Bound-cognate ligand similarity is a useful metric for ranking PDB structures
Only 26% of enzyme structures in the PDB have bound-cognate ligand similarity ≥0.7
We provide rank-ordered lists of PDBs with the most biologically relevant ligands
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