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Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study

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Abstract

Strong and weak hydrogen bonds between protein and ligand are analyzed in a group of 233 X-ray crystal structures of the kinase family. These kinases are from both eukaryotic and prokaryotic organisms. The dataset comprises of 44 sub-families, out of which 35 are of human origin and the rest belong to other organisms. Interaction analysis was carried out in the active sites, defined here as a sphere of 10 Å radius around the ligand. A majority of the interactions are observed between the main chain of the protein and the ligand atoms. As a donor, the ligand frequently interacts with amino acid residues like Leu, Glu and His. As an acceptor, the ligand interacts often with Gly, and Leu. Strong hydrogen bonds N–H···O, O–H···O, N–H···N and weak bonds C–H···O, C–H···N are common between the protein and ligand. The hydrogen bond donor capacity of Gly in N–H···O and C–H···O interactions is noteworthy. Similarly, the acceptor capacity of main chain Glu is ubiquitous in several kinase sub-families. Hydrogen bonds between protein and ligand form characteristic hydrogen bond patterns (supramolecular synthons). These synthon patterns are unique to each sub-family. The synthon locations are conserved across sub-families due to a higher percentage of conserved sequences in the active sites. The nature of active site water molecules was studied through a novel classification scheme, based on the extent of exposure of water molecules. Water which is least exposed usually participates in hydrogen bond formation with the ligand. These findings will help structural biologists, crystallographers and medicinal chemists to design better kinase inhibitors.

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Abbreviations

PKs:

Protein kinases

PKR:

Protein kinase resource

PDB:

Protein Data Bank

HBAT:

Hydrogen bond analysis tool

SVL:

Scientific vector language

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Acknowledgments

S. K. P. thanks Prof. Gautam R. Desiraju, School of Chemistry, University of Hyderabad, Hyderabad, for his helpful guidance in preparing the manuscript. S. K. P. also thanks the chemical computing group (CCG) for technical support and CSIR for fellowship.

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  1. School of Chemistry, University of Hyderabad, Hyderabad, 500 046, India

    Sunil K. Panigrahi

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Correspondence to Sunil K. Panigrahi.

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Panigrahi, S.K. Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study. Amino Acids 34, 617–633 (2008). https://doi.org/10.1007/s00726-007-0015-4

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