The environment of amide groups in protein–ligand complexes: H-bonds and beyond

Abstract

A comprehensive structural analysis of interactions involving amide NH and C=O groups in protein–ligand complexes has been performed based on 3,275 published crystal structures (resolution≤2.5 Å). Most of the amide C=O and NH groups at the protein–ligand interface are highly buried within the binding site and involved in H-bonds with corresponding counter-groups. Small percentages of C=O and NH groups are solvated or embedded in hydrophobic environments. In particular, C=O groups show a higher propensity to be solvated or embedded in a hydrophobic environment than NH groups do. A small percentage of carbonyl groups is involved in weak hydrogen bonds with CH. Cases of dipolar interactions, involving carbonyl oxygen and electrophilic carbon atoms, such as amide, amidinium, guanidium groups, are also identified. A higher percentage of NH are in contact with aromatic carbons, interacting either through hydrogen bonds (preferably with the NH group pointing towards a ring carbon atom) or through stacking between amide plane and ring plane. Comprehensive studies such as the present one are thought to be important for future improvements in the molecular design area, in particular for the development of new scoring functions. Figure Example of dipolar interactions between carbonyl oxygen and amide carbons. a Dipolar (O carbonyl and C amide) interaction within an interaction network (red line H-bonds, blue line dipolar interaction). Protein: PDB 1a4h, [28] N terminal domain of the yeast HSP90 chaperone in complex with geldanamycin; b Dipolar interaction not in an interaction network (red line H-bonds, blue line dipolar interaction). Protein: PDB 1ezq, [29] Factor Xa