Influence of the Solvent Water Molecules at the Active Site of CDK2 on the Binding Free Energy of CDK2-ligand Complexes:  an MM/PBSA Study

Acta Chimica Sinica ›› 2009, Vol. 67 ›› Issue (3): 255-260. Previous Articles Next Articles

Original Articles

应用MM/PBSA方法研究CDK2活性口袋内溶剂水分子对CDK2-配体结合自由能的影响

杨丽君a,b 贾若a 杨胜勇*,a

(a四川大学华西医院生物治疗国家重点实验室成都 610041)
(b西华师范大学化学化工学院南充 637002)

投稿日期:2008-06-10 修回日期:2008-08-27 发布日期:2009-02-14
通讯作者: 杨胜勇

Influence of the Solvent Water Molecules at the Active Site of CDK2 on the Binding Free Energy of CDK2-ligand Complexes: an MM/PBSA Study

Yang, Lijun ^a,b Jia, Ruo ^a Yang, Shengyong ^*,a

(a State Key Laboratory of Biotherapy, West China Hospital, West China Medical School,
Sichuan University, Chengdu 610041)
(b College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002)

Received:2008-06-10 Revised:2008-08-27 Published:2009-02-14
Contact: Yang, Shengyong

Abstract

An MM/PBSA method has been used to investigate the influence of the solvent water molecules at the active site of CDK2 on the binding free energy of CDK2-ligand complexes. The results show that the solvent water molecules at the active site of CDK2 have some contribution to the binding free energy of CDK2-ligand complex. However, the magnitude of contribution depends on the characteristic of the corresponding ligand. The difference of the contribution is mainly due to the different hydrogen bonding interaction network formed among the water molecules, the protein residues and ligand.

Key words: MM/PBSA, CDK2, binding free energy, solvent water molecule, molecular dynamics

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应用MM/PBSA方法研究CDK2活性口袋内溶剂水分子对CDK2-配体结合自由能的影响

Influence of the Solvent Water Molecules at the Active Site of CDK2 on the Binding Free Energy of CDK2-ligand Complexes: an MM/PBSA Study

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