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J Med Chem. 2004 Apr 8;47(8):1879-81.

Discovery of a novel binding trench in HIV integrase.

Author information

  • 1Department of Pharmacology, Howard Hughes Medical Institute, University of California-San Diego, La Jolla, CA 92093-0365, USA.


Docking of the 5CITEP inhibitor to snapshots of a 2 ns HIV-1 integrase MD trajectory indicated a previously uncharacterized trench adjacent to the active site that intermittently opens. Further docking studies of novel ligands with the potential to bind to both regions showed greater selective affinity when able to bind to the trench. Our ranking of ligands is open to experimental testing, and our approach suggests a new target for HIV-1 therapeutics.

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