Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study.
A 2 ns molecular dynamics simulation has been carried out for the HIV-1 integrase-5CITEP complex in order to understand the role of water in defining the ligand's binding mode and to address issues of binding site flexibility and ligand motion. Although the ligand retains considerable mobility within the active site, a structural water molecule bridging 5CITEP with Asp 64 and Asn 155 is identified in the simulation. Consideration of this water molecule could open a route to new HIV-1 integrase inhibitors.
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Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA. hni@mccammon.ucsd.edu
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D001665:Binding Sites; D019427:HIV Integrase / Q000737:chemistry*; D019428:HIV Integrase Inhibitors / Q000737:chemistry*; D007211:Indoles / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D013777:Tetrazoles / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
C400757:1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)propenone; D019428:HIV Integrase Inhibitors; D007211:Indoles; D008024:Ligands; D013777:Tetrazoles; D014867:Water; D019427:HIV Integrase