Crystal structure analysis of HIV-1 protease mutant V82A with a inhibitor saquinavir

Experimental Data Snapshot

  • Resolution: 0.97 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 

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Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir.

Tie, Y.Kovalevsky, A.Y.Boross, P.Wang, Y.F.Ghosh, A.K.Tozser, J.Harrison, R.W.Weber, I.T.

(2007) Proteins 67: 232-242

  • DOI: https://doi.org/10.1002/prot.21304
  • Primary Citation of Related Structures:  
    2NMY, 2NMZ, 2NNK, 2NNP, 3OXC

  • PubMed Abstract: 

    Saquinavir (SQV), the first antiviral HIV-1 protease (PR) inhibitor approved for AIDS therapy, has been studied in complexes with PR and the variants PR(I) (84V) and PR(V) (82A) containing the single mutations I84V and V82A that provide resistance to all the clinical inhibitors. Atomic resolution crystal structures (0.97-1.25 A) of the SQV complexes were analyzed in comparison to the protease complexes with darunavir, a new drug that targets resistant HIV, in order to understand the molecular basis of drug resistance. PR(I) (84V) and PR(V) (82A) complexes were obtained in both the space groups P2(1)2(1)2 and P2(1)2(1)2(1), which provided experimental limits for the conformational flexibility. The SQV interactions with PR were very similar in the mutant complexes, consistent with the similar inhibition constants. The mutation from bigger to smaller amino acids allows more space to accommodate the large group at P1' of SQV, unlike the reduced interactions observed in darunavir complexes. The residues 79-82 have adjusted to accommodate the large hydrophobic groups of SQV, suggesting that these residues are intrinsically flexible and their conformation depends more on the nature of the inhibitor than on the mutations in this region. This analysis will assist with development of more effective antiviral inhibitors.

  • Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: gag
Find proteins for Q7SSI0 (Human immunodeficiency virus 1)
Explore Q7SSI0 
Go to UniProtKB:  Q7SSI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SSI0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ROC

Download Ideal Coordinates CCD File 
F [auth B](2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
C38 H50 N6 O5
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
ROC BindingDB:  2NMZ Ki: min: 0.04, max: 138 (nM) from 29 assay(s)
Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 46 assay(s)
ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 48 assay(s)
ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 41 assay(s)
PDBBind:  2NMZ Ki: 4.3 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 0.97 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.131α = 90
b = 58.588β = 90
c = 61.61γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MAR345data collection
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.6: 2023-12-27
    Changes: Data collection