C─H⋯O hydrogen bonds in kinase-inhibitor interfaces.

C─H⋯O hydrogen bonds constitute a unique class of cohesive interactions. Their properties are similar to those of canonical H-bonds, although their energy is significantly lower, typically in the 0.5-2.5 kcal/mol range. Polarised C─H groups, such as those adjacent to electronegative groups, or within aromatic moieties, are particularly strong donors. C─H⋯O bonds are ubiquitous in nucleic acids and in proteins, notably stabilizing the β-sheet secondary structure. They have also been observed in numerous protein-ligand interactions. Here, we analysed crystal structures, deposited in the Protein Data Bank, of complexes of FDA-approved protein kinase inhibitors with cognate kinases, to assess the possible role of C─H ⋯O hydrogen bonds. The conserved hinge motif of protein kinases with two solvent-exposed carbonyl groups and one exposed backbone amide, is well known to be involved in canonical H-bonding with inhibitors. We now find that in virtually all complexes where the inhibitor interacts with the hinge backbone, at least one of the hinge carbonyl groups accepts an H-bond from a C─H inhibitor group, which is either aromatic or adjacent to an electronegative group. These observations are important for design of hinge-binding scaffolds of novel kinase inhibitors for therapeutic use.