2HS1

Ultra-high resolution X-ray crystal structure of HIV-1 protease V32I mutant with TMC114 (darunavir) inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.84 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.Louis, J.M.Harrison, R.W.Weber, I.T.

(2006) J Mol Biol 363: 161-173

  • DOI: 10.1016/j.jmb.2006.08.007
  • Structures With Same Primary Citation

  • PubMed 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 V3 ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: GAGpol
EC: 3.4.23.16
Find proteins for Q7SSI0 (Human immunodeficiency virus 1)
Explore Q7SSI0 
Go to UniProtKB:  Q7SSI0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download CCD File 
A, B
(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
DMS
Query on DMS

Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
017EC50:  0.25   nM  BindingDB
017Ki:  0.800000011920929   nM  BindingDB
017Ki:  6.599999904632568   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
17Ki :  3.299999952316284   nM  PDBBind
017EC50:  1.600000023841858   nM  BindingDB
017Ki:  0.2199999988079071   nM  BindingDB
017Ki:  3.299999952316284   nM  Binding MOAD
017Ki:  2   nM  BindingDB
017Kd:  0.019999999552965164   nM  BindingDB
017Ki:  0.029999999329447746   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
017Ki:  0.019999999552965164   nM  BindingDB
017IC50:  0.05999999865889549   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.84 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.7α = 90
b = 65.923β = 90
c = 92.534γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance