3EBZ: High Resolution Hiv-2 Protease Structure In Complex With Clinical Drug Darunavir

No drug has been targeted specifically for HIV-2 (human immunodeficiency virus type 2) infection despite its increasing prevalence worldwide. The antiviral HIV-1 (human immunodeficiency virus type 1) protease (PR) inhibitor darunavir and the chemically related GRL98065 and GRL06579A were designed with the same chemical scaffold and different substituents at P2 and P2' to optimize polar interactions for HIV-1 PR (PR1). These inhibitors are also effective antiviral agents for HIV-2-infected cells. Therefore, crystal structures of HIV-2 PR (PR2) complexes with the three inhibitors have been solved at 1.2-A resolution to analyze the molecular basis for their antiviral potency. Unusually, the crystals were grown in imidazole and zinc acetate buffer, which formed interactions with the PR2 and the inhibitors. Overall, the structures were very similar to the corresponding inhibitor complexes of PR1 with an RMSD of 1.1 A on main-chain atoms. Most hydrogen-bond and weaker C-H...O interactions with inhibitors were conserved in the PR2 and PR1 complexes, except for small changes in interactions with water or disordered side chains. Small differences were observed in the hydrophobic contacts for the darunavir complexes, in agreement with relative inhibition of the two PRs. These near-atomic-resolution crystal structures verify the inhibitor potency for PR1 and PR2 and will provide the basis for the development of antiviral inhibitors targeting PR2.
PDB ID: 3EBZDownload
MMDB ID: 66794
PDB Deposition Date: 2008/8/28
Updated in MMDB: 2008/12
Experimental Method:
x-ray diffraction
Resolution: 1.2  Å
Source Organism:
Similar Structures:
Biological Unit for 3EBZ: dimeric; determined by author and by software (PISA)
Molecular Components in 3EBZ
Label Count Molecule
Proteins (2 molecules)
Molecule annotation
Chemicals (25 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB