PMID-sentid	Pub_year	Sent_text		comp_official_name	comp_offsetprotein_name	organism	prot_offset
27481520-7	2013	Besides the hydrogen bond formation, the van der Waals interactions between residues Ile10, Val18, and Leu133 of CDK5 and inhibitors were discovered to constitute another substantial component of their binding mode.	Hydrogen	12-20	cyclin dependent kinase 5	Homo sapiens	113-117	
24085300-7	2013	Based on the crystal structures of the p25 (p35 C-terminal region including AD)-Cdk5 complex, we simulated the three-dimensional structure of the p39 AD-Cdk5 complex and found differences in the hydrogen bond network between Cdk5 and its activators.	Hydrogen	195-203	cyclin dependent kinase 5	Homo sapiens	80-84	
24085300-7	2013	Based on the crystal structures of the p25 (p35 C-terminal region including AD)-Cdk5 complex, we simulated the three-dimensional structure of the p39 AD-Cdk5 complex and found differences in the hydrogen bond network between Cdk5 and its activators.	Hydrogen	195-203	cyclin dependent kinase 5	Homo sapiens	153-157	
24085300-7	2013	Based on the crystal structures of the p25 (p35 C-terminal region including AD)-Cdk5 complex, we simulated the three-dimensional structure of the p39 AD-Cdk5 complex and found differences in the hydrogen bond network between Cdk5 and its activators.	Hydrogen	195-203	cyclin dependent kinase 5	Homo sapiens	153-157	
24085300-8	2013	Three amino acids of p35, Asp-259, Asn-266, and Ser-270, which are involved in hydrogen bond formation with Cdk5, are changed to Gln, Gln, and Pro in p39.	Hydrogen	79-87	cyclin dependent kinase 5	Homo sapiens	108-112	
24085300-9	2013	Because these three amino acids in p39 do not participate in hydrogen bond formation, we predicted that the number of hydrogen bonds between p39 and Cdk5 was reduced compared with p35 and Cdk5.	Hydrogen	118-126	cyclin dependent kinase 5	Homo sapiens	149-153	
24085300-10	2013	Using substitution mutants, we experimentally validated that the difference in the hydrogen bond network contributes to the different properties between Cdk5 and its activators.	Hydrogen	83-91	cyclin dependent kinase 5	Homo sapiens	153-157	
33155527-8	2022	On the basis of various MD analysis like RMSD, RMSF, Rg, SASA, Number of hydrogen bonds, Principal component analysis and binding free energy (CDK5-ZINC6261568: -129.50 kJ.mol-1 and CDK5-ZINC14168360: -191.16 kJ.mol-1), we have found that ZINC6261568 and ZINC14168360 can act as a lead compound against the CDK5.	Hydrogen	73-81	cyclin dependent kinase 5	Homo sapiens	143-147	
31073393-12	2019	During 30 ns simulation, the candidate inhibitors established <3.0 A root mean square deviation and stable hydrogen bond interactions with the ATP-binding site residues of Cdk5/p25.	Hydrogen	110-118	cyclin dependent kinase 5	Homo sapiens	175-179	
20013135-3	2010	Based on systematic examination of hydrogen bond breaking and classical MD/molecular mechanics-generalized Born/surface area) (MM-GBSA) calculations, a CDK5 activation mechanism by p25 is suggested.	Hydrogen	35-43	cyclin dependent kinase 5	Homo sapiens	152-156	
17713901-3	2007	Together with previous results, the current work shows a highly conserved water-involved hydrogen bonding (HB) network in both CDK2- and CDK5-indirubin combinations to complete information from the X-ray crystallography.	Hydrogen	89-97	cyclin dependent kinase 5	Homo sapiens	137-141	
16494969-6	2006	Docking of 2-[[-5-bromo-2-oxoindolin-3-ylidene]amino]-3-(1H-imidazol2-yl)propanoic acid 14 to CDK5/p25 indicates that this compound can interact with the enzyme through four hydrogen bonds; for GSK/3beta, the ligand poses itself in another orientation, also four hydrogen bonds can be formed between the ligand and the receptor, otherwise hydrophobic interactions seem to predominate.	Hydrogen	174-182	cyclin dependent kinase 5	Homo sapiens	94-98	
16494969-6	2006	Docking of 2-[[-5-bromo-2-oxoindolin-3-ylidene]amino]-3-(1H-imidazol2-yl)propanoic acid 14 to CDK5/p25 indicates that this compound can interact with the enzyme through four hydrogen bonds; for GSK/3beta, the ligand poses itself in another orientation, also four hydrogen bonds can be formed between the ligand and the receptor, otherwise hydrophobic interactions seem to predominate.	Hydrogen	263-271	cyclin dependent kinase 5	Homo sapiens	94-98