3 years ago

Discovering protein−ligand chalcogen bonding in the protein data bank using endocyclic sulfur-containing heterocycles as ligand search subsets

Miguel O. Mitchell

Abstract

The chalcogen bond, the noncovalent, electrostatic attraction between covalently bonded atoms in group 16 and Lewis bases, is present in protein−ligand interactions based on X-ray structures deposited in the Protein Data Bank (PDB). Discovering protein−ligand chalcogen bonding in the PDB employed a strategy that focused on searching the database for protein complexes of five-membered, heterocyclic ligands containing endocyclic sulfur with endo electron-withdrawing groups (isothiazoles; thiazoles; 1,2,3-, 1,2.4-, 1,2,5-, 1,3,4-thiadiazoles) and thiophenes with exo electron-withdrawing groups, e.g., 2-chloro, 2-bromo, 2-amino, 2-alkylthio. Out of 930 ligands investigated, 33 or 3.5% have protein−ligand S---O interactions of which 31 are chalcogen bonds and two appear to be S---HO hydrogen bonds. The bond angles for some of the chalcogen bonds found in the PDB are less than 90°, and an electrostatic model is proposed to explain this phenomenon.

Publisher URL: https://link.springer.com/article/10.1007/s00894-017-3452-3

DOI: 10.1007/s00894-017-3452-3

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