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

Amino Acids
Sunil K Panigrahi

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 A 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 per...Continue Reading

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Citations

Feb 4, 2012·Amino Acids·Srđan Ð StojanovićBožidarka L Zarić
Feb 12, 2013·Journal of Chemical Information and Modeling·Guo-Bo LiSheng-Yong Yang
Sep 21, 2013·Nucleic Acids Research·Stacey M SouthallJon R Wilson
Jan 11, 2012·Journal of Computer-aided Molecular Design·Oliver KorbThomas E Exner
Oct 4, 2013·Journal of Molecular Recognition : JMR·Sreekanth RajanHo Sup Yoon
May 16, 2011·Molecular Informatics·Srđan Đ StojanovićBožidarka L Zarić
Jun 11, 2015·Journal of Molecular Graphics & Modelling·Amen ShamimSyed Sikander Azam
Apr 23, 2011·The Journal of Physical Chemistry. B·Yuheng YaoMingdong Dong
Jan 13, 2017·Journal of the American Chemical Society·Subhankar Saha, Gautam R Desiraju
Apr 10, 2020·IUBMB Life·Zygmunt S DerewendaUrszula Derewenda
May 31, 2018·Journal of Computer-aided Molecular Design·Thandokuhle NtombelaBahareh Honarparvar
Mar 7, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Joanna BojarskaWojciech M Wolf
Jul 13, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alexander Eisold, Dirk Labudde
Apr 1, 2021·Network Modeling and Analysis in Health Informatics and Bioinformatics·Inemesit A UdofiaChukwuemeka Isanbor

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