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 

wwPDB Validation   3D Report Full Report

This is version 1.4 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: 10.1128/jvi.77.2.1306-1315.2003
  • Primary Citation of Related Structures:  
    1MT7, 1N49, 1MT9, 1MT8, 1MTB

  • 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 patien ...

    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.

    Related Citations: 
    • How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease
      Prabu-Jeyabalan, M., Nalivaika, E., Schiffer, C.A.
      (2000) J Mol Biol 301: 1207
    • Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes
      Prabu-Jeyabalan, M., Nalivaika, E., Schiffer, C.A.
      (2002) Structure 10: 369
    • Lack of synergy for inhibitors targeting a multi-drug resistant HIV-1 protease
      King, N.M., Melnick, L., Prabu-Jeyabalan, M., Nalivaika, E.A., Yang, S.S., Gao, Y., Nie, X., Zepp, C., Heefner, D.L., Schiffer, C.A.
      (2002) Protein Sci 11: 418
    • ABT-538 Is a Potent Inhibitor of Human Immunodeficiency Virus Protease and has High Oral Bioavailability in Humans
      Kempf, D.J., Marsh, K.C., Denissen, J.F., McDonald, E., Vasavanonda, S., Flentge, C.A., Green, B.E., Fino, L., Park, C.H., Kong, X., Wideburg, N.E., Saldivar, A., Ruiz, L., Kati, W.M., Sham, H.L., Robins, T., Stewart, K.D., Hsu, A., Plattner, J.J., Leonard, J.M., Norbeck, D.W.
      (1995) Proc Natl Acad Sci U S A 92: 2484

    Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseABCD99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: POL
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on RIT

Download CCD File 
B, D
C37 H48 N6 O5 S2
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RITΔH:  17.969999313354492   kJ/mol  BindingDB
RITΔG:  52.66999816894531   kJ/mol  BindingDB
RITΔH:  15.050000190734863   kJ/mol  BindingDB
RIT-TΔS:  57.29999923706055   kJ/mol  BindingDB
RITΔG:  57.68000030517578   kJ/mol  BindingDB
RITΔG:  41.79999923706055   kJ/mol  BindingDB
RIT-TΔS:  80.29000091552734   kJ/mol  BindingDB
RITΔH:  0.07999999821186066   kJ/mol  BindingDB
RIT-TΔS:  52.68000030517578   kJ/mol  BindingDB
RITIC50:  67   nM  BindingDB
RIT-TΔS:  42.25   kJ/mol  BindingDB
RITΔH:  33.439998626708984   kJ/mol  BindingDB
RITΔH:  73.1500015258789   kJ/mol  BindingDB
RITΔH:  26.75   kJ/mol  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RIT-TΔS:  82.80000305175781   kJ/mol  BindingDB
RIT-TΔS:  34.70000076293945   kJ/mol  BindingDB
RITΔH:  8.359999656677246   kJ/mol  BindingDB
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RIT-TΔS:  64.81999969482422   kJ/mol  BindingDB
RIT-TΔS:  58.59000015258789   kJ/mol  BindingDB
RITΔH:  51   kJ/mol  BindingDB
RITΔH:  8.779999732971191   kJ/mol  BindingDB
RIT-TΔS:  43.08000183105469   kJ/mol  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RITKi:  0.5   nM  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RITKi:  30   nM  BindingDB
RITΔG:  42.63999938964844   kJ/mol  BindingDB
RITΔH:  9.609999656677246   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RIT-TΔS:  56.86000061035156   kJ/mol  BindingDB
RITΔG:  45.97999954223633   kJ/mol  BindingDB
RITΔG:  44.72999954223633   kJ/mol  BindingDB
RITKi:  23   nM  BindingDB
RIT-TΔS:  65.23999786376953   kJ/mol  BindingDB
RITΔH:  14.630000114440918   kJ/mol  BindingDB
RITΔG:  44.310001373291016   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RIT-TΔS:  64.81999969482422   kJ/mol  BindingDB
RITKi:  40   nM  BindingDB
RITΔG:  55.59000015258789   kJ/mol  BindingDB
RITΔG:  54.34000015258789   kJ/mol  BindingDB
RIT-TΔS:  50.27000045776367   kJ/mol  BindingDB
RITΔG:  53.91999816894531   kJ/mol  BindingDB
RITKi:  0.3700000047683716   nM  BindingDB
RITKi:  15   nM  BindingDB
RITΔG:  57.27000045776367   kJ/mol  BindingDB
RITΔH:  9.199999809265137   kJ/mol  BindingDB
RIT-TΔS:  46.84000015258789   kJ/mol  BindingDB
RITΔH:  25.079999923706055   kJ/mol  BindingDB
RITΔH:  3.759999990463257   kJ/mol  BindingDB
RIT-TΔS:  57.33000183105469   kJ/mol  BindingDB
RITKi:  0.05999999865889549   nM  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITΔH:  17.559999465942383   kJ/mol  BindingDB
RITKi:  4   nM  BindingDB
RITKi:  0.5899999737739563   nM  BindingDB
RITΔH:  11.699999809265137   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITKi:  4.5   nM  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RIT-TΔS:  62.7599983215332   kJ/mol  BindingDB
RIT-TΔS:  36.369998931884766   kJ/mol  BindingDB
RIT-TΔS:  70.2699966430664   kJ/mol  BindingDB
RITΔG:  49.7400016784668   kJ/mol  BindingDB
RITKi:  0.11999999731779099   nM  BindingDB
RITΔH:  24.239999771118164   kJ/mol  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RITΔH:  2.930000066757202   kJ/mol  BindingDB
RIT-TΔS:  66.48999786376953   kJ/mol  BindingDB
RITΔG:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  39.29999923706055   kJ/mol  BindingDB
RIT-TΔS:  51.0099983215332   kJ/mol  BindingDB
RIT-TΔS:  75.27999877929688   kJ/mol  BindingDB
RITΔH:  4.599999904632568   kJ/mol  BindingDB
RITΔH:  2.0899999141693115   kJ/mol  BindingDB
RITΔH:  12.539999961853027   kJ/mol  BindingDB
RITΔH:  13.789999961853027   kJ/mol  BindingDB
RITKi:  2.809999942779541   nM  BindingDB
RITΔG:  51.83000183105469   kJ/mol  BindingDB
RITKi:  0.46000000834465027   nM  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RITΔG:  56.0099983215332   kJ/mol  BindingDB
RIT-TΔS:  60.63999938964844   kJ/mol  BindingDB
RITΔH:  30.510000228881836   kJ/mol  BindingDB
RITKd:  0.6100000143051147   nM  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RITΔG:  40.959999084472656   kJ/mol  BindingDB
RITΔG:  39.709999084472656   kJ/mol  BindingDB
RITKi:  2.4000000953674316   nM  BindingDB
RIT-TΔS:  45.59000015258789   kJ/mol  BindingDB
RIT-TΔS:  58.560001373291016   kJ/mol  BindingDB
RITΔG:  36.779998779296875   kJ/mol  BindingDB
RITKi:  0.15000000596046448   nM  BindingDB
RITΔG:  34.279998779296875   kJ/mol  BindingDB
RITKi:  0.029999999329447746   nM  BindingDB
RITKi:  3.0199999809265137   nM  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RITKi:  60   nM  BindingDB
RITΔG:  50.15999984741211   kJ/mol  BindingDB
RITΔG:  45.13999938964844   kJ/mol  BindingDB
RITΔG:  38.869998931884766   kJ/mol  BindingDB
RITΔH:  43.470001220703125   kJ/mol  BindingDB
RITKd:  0.6000000238418579   nM  BindingDB
RITΔH:  35.95000076293945   kJ/mol  BindingDB
RIT-TΔS:  69.83000183105469   kJ/mol  BindingDB
RIT-TΔS:  76.54000091552734   kJ/mol  BindingDB
RITΔG:  60.189998626708984   kJ/mol  BindingDB
RITΔG:  56.43000030517578   kJ/mol  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITΔG:  43.470001220703125   kJ/mol  BindingDB
RIT-TΔS:  33.040000915527344   kJ/mol  BindingDB
RITKi:  0.9100000262260437   nM  BindingDB
RIT-TΔS:  43.91999816894531   kJ/mol  BindingDB
RITΔG:  31.770000457763672   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RITΔG:  28.84000015258789   kJ/mol  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RITΔH:  0   kJ/mol  BindingDB
RIT-TΔS:  102.05999755859375   kJ/mol  BindingDB
RITΔG:  36.369998931884766   kJ/mol  BindingDB
RITΔH:  27.59000015258789   kJ/mol  BindingDB
RITKi:  109   nM  BindingDB
RIT-TΔS:  44.75   kJ/mol  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RIT-TΔS:  42.63999938964844   kJ/mol  BindingDB
RITΔH:  22.56999969482422   kJ/mol  BindingDB
RIT-TΔS:  46.41999816894531   kJ/mol  BindingDB
RITΔG:  33.439998626708984   kJ/mol  BindingDB
RITΔG:  38.040000915527344   kJ/mol  BindingDB
RITKi:  1.100000023841858   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
B, DRITONAVIRPeptide-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 

  • 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