Viability of a Drug-Resistant HIV-1 Protease Variant: Structural Insights for Better Anti-Viral Therapy

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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This is version 1.6 of the entry. See complete history


Viability of a Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variant: Structural Insights for Better Antiviral Therapy

Prabu-Jeyabalan, M.Nalivaika, E.A.King, N.M.Schiffer, C.A.

(2003) J Virol 77: 1306-1315

  • DOI: https://doi.org/10.1128/jvi.77.2.1306-1315.2003
  • Primary Citation of Related Structures:  
    1MT7, 1MT8, 1MT9, 1MTB, 1N49

  • PubMed Abstract: 

    Under the selective pressure of protease inhibitor therapy, patients infected with human immunodeficiency virus (HIV) often develop drug-resistant HIV strains. One of the first drug-resistant mutations to arise in the protease, particularly in patients receiving indinavir or ritonavir treatment, is V82A, which compromises the binding of these and other inhibitors but allows the virus to remain viable. To probe this drug resistance, we solved the crystal structures of three natural substrates and two commercial drugs in complex with an inactive drug-resistant mutant (D25N/V82A) HIV-1 protease. Through structural analysis and comparison of the protein-ligand interactions, we found that Val82 interacts more closely with the drugs than with the natural substrate peptides. The V82A mutation compromises these interactions with the drugs while not greatly affecting the substrate interactions, which is consistent with previously published kinetic data. Coupled with our earlier observations, these findings suggest that future inhibitor design may reduce the probability of the appearance of drug-resistant mutations by targeting residues that are essential for substrate recognition.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01605, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: POL
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03369
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RIT

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
C37 H48 N6 O5 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
RIT BindingDB:  1N49 Ki: min: 0.01, max: 109 (nM) from 27 assay(s)
Kd: min: 0.6, max: 0.61 (nM) from 2 assay(s)
IC50: 67 (nM) from 1 assay(s)
-TΔS: min: -1.02e+2, max: -3.01e+1 (kJ/mol) from 37 assay(s)
ΔH: min: -2.76e+1, max: 73.15 (kJ/mol) from 38 assay(s)
ΔG: min: -6.02e+1, max: -2.88e+1 (kJ/mol) from 36 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
E [auth B],
F [auth D]
RITONAVIRPeptide-like / Inhibitor
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.62α = 90
b = 61.35β = 81.2
c = 59.04γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-02-14
    Changes: Data collection, Refinement description