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Discovering protein−ligand chalcogen bonding in the protein data bank using endocyclic sulfur-containing heterocycles as ligand search subsets.
- Source :
-
Journal of Molecular Modeling . Oct2017, Vol. 23 Issue 10, p1-12. 12p. - Publication Year :
- 2017
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 16102940
- Volume :
- 23
- Issue :
- 10
- Database :
- Academic Search Index
- Journal :
- Journal of Molecular Modeling
- Publication Type :
- Academic Journal
- Accession number :
- 125840039
- Full Text :
- https://doi.org/10.1007/s00894-017-3452-3