Analysis of CDK2 active-site hydration: A method to design new inhibitors

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F04%3A00009962" target="_blank" >RIV/00216224:14310/04:00009962 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15310/04:00002156

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Analysis of CDK2 active-site hydration: A method to design new inhibitors

Original language description

The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine co

Czech name

Analýza hydratace CDK2 aktivního místa

Czech description

The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine co

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

<a href="/en/project/GV201%2F98%2FK041" target="_blank" >GV201/98/K041: HCILAB - human - computer interactions laboratory</a><br>

Continuities

Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2004

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Proteins: Structure, Function, and Bioinformatics

ISSN

0887-3585

e-ISSN

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Volume of the periodical

55

Issue of the periodical within the volume

3

Country of publishing house

CZ - CZECH REPUBLIC

Number of pages

17

Pages from-to

258-274

UT code for WoS article

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EID of the result in the Scopus database

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