1HVS

STRUCTURAL BASIS OF DRUG RESISTANCE FOR THE V82A MUTANT OF HIV-1 PROTEASE: BACKBONE FLEXIBILITY AND SUBSITE REPACKING

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase.

Baldwin, E.T., Bhat, T.N., Liu, B., Pattabiraman, N., Erickson, J.W.

(1995) Nat Struct Biol 2: 244-249

  • DOI: 10.1038/nsb0395-244
  • Primary Citation of Related Structures:  
    1HVS

  • PubMed Abstract: 

    • A major problem in the development of antiviral therapies for AIDS has been the emergence of drug resistance. We report an analysis of the structure of a Val 82 to Ala mutant of HIV-1 proteinase complexed to A-77003, a C2 symmetry-based inhibitor. Modelling studies predicted that the V82A mutation would result in decreased van der Waals' interactions with the phenyl rings of A-77003 in both S1 and S1' subsites ...

    A major problem in the development of antiviral therapies for AIDS has been the emergence of drug resistance. We report an analysis of the structure of a Val 82 to Ala mutant of HIV-1 proteinase complexed to A-77003, a C2 symmetry-based inhibitor. Modelling studies predicted that the V82A mutation would result in decreased van der Waals' interactions with the phenyl rings of A-77003 in both S1 and S1' subsites. Unexpected rearrangements of the protein backbone, however, resulted in favourable re-packing of inhibitor and enzyme atoms in the S1 but not the S1' subsite. This analysis reveals the importance of enzyme flexibility in accommodating alternate packing arrangements, and can be applied to the re-design of inhibitors targeted to drug resistant variants which emerge in the clinic.

    Related Citations: 
    • Influence of Stereochemistry on Activity and Binding Modes for C2 Symmetry-Based Diol Inhibitors of HIV-1 Protease
      Hosur, M.V., Bhat, T.N., Kempf, D.J., Baldwin, E.T., Liu, B., Gulnik, S., Wideburg, N.E., Norbeck, D.W., Appelt, K., Erickson, J.W.
      (1994) J Am Chem Soc 116: 847
    • Structure-Based Inhibitors of HIV-1 Protease
      Wlodawer, A., Erickson, J.W.
      (1993) Annu Rev Biochem 62: 543
    Organizational Affiliation: 

    Frederick Biomedical Supercomputing Center, PRI/DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEA, B99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Explore P04587 
Go to UniProtKB:  P04587
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04587
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A77
Query on A77
Download Ideal Coordinates CCD File 
C [auth A]N-{1-BENZYL-(2R,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE
C44 H58 N8 O6
QPVWMQXBTCSLCB-BYAJYZPISA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
A77 Binding MOAD:  1HVS Ki: 0.05 (nM) from 1 assay(s)
BindingDB:  1HVS Ki: 0.01 (nM) from 1 assay(s)
Kd: 0.08 (nM) from 1 assay(s)
IC50: 1 (nM) from 1 assay(s)
PDBBind:  1HVS Ki: 0.05 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 59.6β = 90
c = 62.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance