PDBsum entry 2hs2

Hydrolase

PDB id: 2hs2

Contents

Protein chains

99 a.a. *

Ligands

017

017-DMS

Metals

_CL ×2

Waters ×213

* Residue conservation analysis

PDB id:

2hs2

Name:

Hydrolase

Title:

Crystal structure of m46l mutant of HIV-1 protease complexed with tmc114 (darunavir)

Structure:

Protease. Chain: a, b. Fragment: HIV-1 protease (residues 500-598). Synonym: retropepsin, pr. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: gag. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.22Å R-factor: 0.142 R-free: 0.195

Authors:

I.T.Weber,A.Y.Kovalevsky,F.Liu

Key ref:

A.Y.Kovalevsky et al. (2006). Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114. J Mol Biol, 363, 161-173. PubMed id: 16962136 DOI: 10.1016/j.jmb.2006.08.007

Date:

20-Jul-06 Release date: 03-Oct-06

Protein chains

Q7SSI0  (Q7SSI0_9HIV1) -  Protease (Fragment) from Human immunodeficiency virus 1

Seq: 99 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

DOI no: 10.1016/j.jmb.2006.08.007

J Mol Biol 363:161-173 (2006)

PubMed id: 16962136

Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114.

A.Y.Kovalevsky, F.Liu, S.Leshchenko, A.K.Ghosh, J.M.Louis, R.W.Harrison, I.T.Weber.

ABSTRACT

TMC114 (darunavir) is a promising clinical inhibitor of HIV-1 protease (PR) for treatment of drug resistant HIV/AIDS. We report the ultra-high 0.84 A resolution crystal structure of the TMC114 complex with PR containing the drug-resistant mutation V32I (PR(V32I)), and the 1.22 A resolution structure of a complex with PR(M46L). These structures show TMC114 bound at two distinct sites, one in the active-site cavity and the second on the surface of one of the flexible flaps in the PR dimer. Remarkably, TMC114 binds at these two sites simultaneously in two diastereomers related by inversion of the sulfonamide nitrogen. Moreover, the flap site is shaped to accommodate the diastereomer with the S-enantiomeric nitrogen rather than the one with the R-enantiomeric nitrogen. The existence of the second binding site and two diastereomers suggest a mechanism for the high effectiveness of TMC114 on drug-resistant HIV and the potential design of new inhibitors.

Selected figure(s)

Figure 2.
Figure 2. Hydrogen bonds between the central OH group of TMC114 and the catalytic Asp25 and Asp25′. The major conformation of TMC114 is colored by atom type, and the minor conformation is green. Interatomic distances are shown in Å. (a) PR-TMC114 (PDB code 1S6G); the TMC114 conformations were refined with 55% and 45% occupancies. (b) PR[V32I]-TMC114 and (c) PR[M46L]-TMC114. The 2F[o]–F[c] electron density for the active site residues Asp25 and Asp25′ is shown with the contour levels of 2.2σ. The alternate conformations have occupancies of 60% and 40%.

Figure 3.
Figure 3. Hydrogen bond, C-H…O and C-H…π interactions are shown in the active site cavity of PR[V32I] for the major conformation of TMC114 (a) and the minor conformation (b). Interactions for the alternate conformations of TMC114 in PR and PR[M46L] are shown in the Supplementary Material.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 363, 161-173) copyright 2006.

Figures were selected by an automated process.