Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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A Simple and Efficient Docking Method to the Cyclin-Dependent Kinase 2

  • Park, Kwang-Su (Division of Bioscience and Biotechnology, Institute of Biomedical Science and Technology, Konkuk University) ;
  • Kim, Jin-Young (Division of Bioscience and Biotechnology, Institute of Biomedical Science and Technology, Konkuk University) ;
  • Chong, You-Hoon (Division of Bioscience and Biotechnology, Institute of Biomedical Science and Technology, Konkuk University) ;
  • Choo, Hyun-Ah (Life Sciences Division, Korea Institute of Science and Technology)
  • Published : 2007.02.20
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Abstract

The subtle but significant differences and thereby the lack of consensus in active site structures among the crystal structures of cyclin-dependent kinase 2 (CDK2) has hampered structure-based drug design. In this study, we devised a simple but effective ‘mutation, pharmacophore-guided docking, followed by mutation' strategy to generate an “average” CDK2 structure, which was used for ligand docking study to successfully reproduce 30 out of 32 X-ray ligand positions within 2.0 A of heavy atom RMSD. This novel docking method was applied for structure-based 3D QSAR with CoMSIA study of a series of structurally related ligands, which showed a good discrimination between CDK2 binders and nonbinders.

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References

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