3CYW

Effect of Flap Mutations on Structure of HIV-1 Protease and Inhibition by Saquinavir and Darunavir

  • Classification: HYDROLASE
  • Mutation(s): Yes 

  • Deposited: 2008-04-27 Released: 2008-05-27 
  • Deposition Author(s): Liu, F., Weber, I.T.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.

Liu, F.Kovalevsky, A.Y.Tie, Y.Ghosh, A.K.Harrison, R.W.Weber, I.T.

(2008) J Mol Biol 381: 102-115

  • DOI: 10.1016/j.jmb.2008.05.062
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently c ...

    HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistant HIV. Structural and kinetic analyses were used to investigate the role of flap residues Gly48, Ile50, and Ile54 in the development of drug resistance. The crystal structures of flap mutants PR(I50V) (PR with I50V mutation), PR(I54V) (PR with I54V mutation), and PR(I54M) (PR with I54M mutation) complexed with saquinavir (SQV) as well as PR(G48V) (PR with G48V mutation), PR(I54V), and PR(I54M) complexed with darunavir (DRV) were determined at resolutions of 1.05-1.40 A. The PR mutants showed changes in flap conformation, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type PR. The PR contacts with DRV were closer in PR(G48V)-DRV than in the wild-type PR-DRV, whereas they were longer in PR(I54M)-DRV. The relative inhibition of PR(I54V) and that of PR(I54M) were similar for SQV and DRV. PR(G48V) was about twofold less susceptible to SQV than to DRV, whereas the opposite was observed for PR(I50V). The observed inhibition was in agreement with the association of G48V and I50V with clinical resistance to SQV and DRV, respectively. This analysis of structural and kinetic effects of the mutants will assist in the development of more effective inhibitors for drug-resistant HIV.


    Related Citations: 
    • Ultra-High Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor Tmc114
      Kovalevsky, A.Y., Liu, F., Leshchenko, S., Ghosh, A.K., Harrison, R.W., Weber, I.T.
      (2006) J Mol Biol 365: 901
    • Kinetic, Stability, and Structural Changes in High-Resolution Crystal Structures of HIV-1 Protease with Drug-Resistant Mutations L24I, I50V, and G73S.
      Liu, F., Boross, P.I., Wang, Y.F., Tozser, J., Louis, J.M., Harrison, R.W., Weber, I.T.
      (2005) J Mol Biol 354: 789

    Organizational Affiliation

    Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Protease
A, B
99N/AMutation(s): 1 
Gene Names: gag-pol
EC: 3.4.23.16
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Go to UniProtKB:  P04587
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download CCD File 
A
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
C27 H37 N3 O7 S
CJBJHOAVZSMMDJ-HEXNFIEUSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
17Ki:  17   nM  PDBBind
017Ki:  17   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.16α = 90
b = 86.25β = 90
c = 45.92γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-04-27 
  • Released Date: 2008-05-27 
  • Deposition Author(s): Liu, F., Weber, I.T.

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance