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    The effect of tightly-bound water molecules on scaffold diversity in computer-aided de novo ligand design of CDK2 inhibitors

    20099_downloaded_stream_87.pdf (729.7Kb)
    Access Status
    Open access
    Authors
    Garcia-sosa, A.
    Mancera, Ricardo
    Date
    2006
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Garcia-sosa, Alfonso and Mancera, Ricardo. 2006. The effect of tightly-bound water molecules on scaffold diversity in computer-aided de novo ligand design of CDK2 inhibitors. Journal of Molecular Modeling 12: 422-431.
    Source Title
    Journal of Molecular Modeling
    DOI
    10.1007/s00894-005-0063-1
    Faculty
    Division of Health Sciences
    School of Pharmacy
    Remarks

    The original publication is available at http://www.springerlink.com

    URI
    http://hdl.handle.net/20.500.11937/29203
    Collection
    • Curtin Research Publications
    Abstract

    We have determined the effects that tightly bound water molecules have on the de novo design of cyclin-dependent kinase-2 (CDK2) ligands. In particular, we have analyzed the impact of a specific structural water molecule on the chemical diversity and binding mode of ligands generated through a de novo structure-based ligand generation method in the binding site of CDK2. The tightly bound water molecule modifies the size and shape of the binding site and we have found that it also imposed constraints on the observed binding modes of the generated ligands. This in turn had the indirect effect of reducing the chemical diversity of the underlying molecular scaffolds that were able to bind to the enzyme satisfactorily.

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