A novel computational analysis of ligand-induced conformational changes in the ATP binding sites of cyclin dependent kinases

Journal of Medicinal Chemistry

Volumn 49, Issue 18, 2006, Pages 5434-5441

  Subramanian, Jyothi ^a   Sharma, Somesh ^a   B Rao, Chandrika ^a  

^a Piramal Enterprises Limited   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CYCLIN DEPENDENT KINASE; CYCLIN DEPENDENT KINASE 2; CYCLIN DEPENDENT KINASE 5; CYCLIN DEPENDENT KINASE 6; LIGAND; LYSINE; PROTEIN KINASE;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; LIGAND BINDING; MACROMOLECULE; PLASTICITY; SIMULATION; STATISTICAL MODEL;

ADENOSINE TRIPHOSPHATE; BINDING SITES; COMPUTER SIMULATION; CYCLIN-DEPENDENT KINASE 2; CYCLIN-DEPENDENT KINASES; LIGANDS; LINEAR MODELS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 33748579250     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm060172s     Document Type: Article

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37. In the case of PDB entry IUNL (CDK5), the residue corresponding to Leu83 is Cys83, and the residue corresponding to Gln131 is Gln130. In the case of PDB entry 1XO2 (CDK6), the residues corresponding to Leu83, Lys89, and Gln131 are Val101, Thr107, and Gln149, respectively. For PDB entry 1GII (ATP binding pocket of CDK2 replaced with CDK4), the residues corresponding to Leu83, Lys89, and Gln131 are Va183, Thr89, and Gln131, respectively. To compute inter-residue distances for these structures, the corresponding atoms were taken. Most importantly, the side chain OH group of the corresponding Thr residue was used in place of the terminal side chain NH of Lys89 in the case of the PDB entries 1XO2 and 1GII.