Comparing the Accumulation of Active Site and Non-active Site Mutations in the HIV-1 Protease

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Comparing the Accumulation of Active- and Nonactive-Site Mutations in the HIV-1 Protease.

Clemente, J.C.Moose, R.E.Hemrajani, R.Whitford, L.R.Govindasamy, L.Reutzel, R.McKenna, R.Agbandje-McKenna, M.Goodenow, M.M.Dunn, B.M.

(2004) Biochemistry 43: 12141-12151

  • DOI: 10.1021/bi049459m
  • Primary Citation of Related Structures:  
    1SH9, 1SGU

  • PubMed Abstract: 
  • Protease inhibitor resistance still poses one of the greatest challenges in treating HIV. To better design inhibitors able to target resistant proteases, a deeper understanding is needed of the effects of accumulating mutations and the contributions ...

    Protease inhibitor resistance still poses one of the greatest challenges in treating HIV. To better design inhibitors able to target resistant proteases, a deeper understanding is needed of the effects of accumulating mutations and the contributions of active- and nonactive-site mutations to the resistance. We have engineered a series of variants containing the nonactive-site mutations M46I and I54V and the active-site mutation I84V. These mutations were added to a protease clone (V6) isolated from a pediatric patient on ritonavir therapy. This variant possessed the ritonavir-resistance-associated mutations in the active-site (V32I and V82A) and nonactive-site mutations (K20R, L33F, M36I, L63P, A71V, and L90M). The I84V mutation had the greatest effect on decreasing catalytic efficiency, 10-fold when compared to the pretherapy clone LAI. The decrease in catalytic efficiency was partially recovered by the addition of mutations M46I and I54V. The M46I and I54V were just as effective at decreasing inhibitor binding as the I84V mutation when compared to V6 and LAI. The V6(54/84) variant showed over 1000-fold decrease in inhibitor-binding strength to ritonavir, indinavir, and nelfinavir when compared to LAI and V6. Crystal-structure analysis of the V6(54/84) variant bound to ritonavir and indinavir shows structural changes in the 80's loops and active site, which lead to an enlarged binding cavity when compared to pretherapy structures in the Protein Data Bank. Structural changes are also seen in the 10's and 30's loops, which suggest possible changes in the dynamics of flap opening and closing.

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA. clemente@ufl.edu

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL polyproteinAB99Human immunodeficiency virus 1Mutation(s): 10 
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on RIT

Download CCD File 
C37 H48 N6 O5 S2
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RITΔH:  2.930000066757202   kJ/mol  BindingDB
RIT-TΔS:  64.81999969482422   kJ/mol  BindingDB
RITKi :  932   nM  PDBBind
RITKi:  0.699999988079071   nM  BindingDB
RITKi:  3.0199999809265137   nM  BindingDB
RITKi:  0.5   nM  BindingDB
RITΔH:  8.359999656677246   kJ/mol  BindingDB
RITΔH:  9.199999809265137   kJ/mol  BindingDB
RIT-TΔS:  46.84000015258789   kJ/mol  BindingDB
RIT-TΔS:  75.27999877929688   kJ/mol  BindingDB
RITΔH:  11.699999809265137   kJ/mol  BindingDB
RITKd:  0.6100000143051147   nM  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RIT-TΔS:  58.59000015258789   kJ/mol  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RIT-TΔS:  80.29000091552734   kJ/mol  BindingDB
RITΔG:  56.43000030517578   kJ/mol  BindingDB
RIT-TΔS:  43.91999816894531   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITKi:  0.5899999737739563   nM  BindingDB
RIT-TΔS:  65.23999786376953   kJ/mol  BindingDB
RITKi:  4   nM  BindingDB
RITKi:  0.05999999865889549   nM  BindingDB
RITKi:  4.5   nM  BindingDB
RIT-TΔS:  39.29999923706055   kJ/mol  BindingDB
RITΔH:  13.789999961853027   kJ/mol  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RITΔG:  49.7400016784668   kJ/mol  BindingDB
RITKi:  0.11999999731779099   nM  BindingDB
RIT-TΔS:  42.63999938964844   kJ/mol  BindingDB
RITIC50:  67   nM  BindingDB
RITΔH:  35.95000076293945   kJ/mol  BindingDB
RITΔG:  28.84000015258789   kJ/mol  BindingDB
RITKi:  1.100000023841858   nM  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITKi:  932   nM  Binding MOAD
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RITKi:  40   nM  BindingDB
RITΔH:  14.630000114440918   kJ/mol  BindingDB
RITΔH:  15.050000190734863   kJ/mol  BindingDB
RIT-TΔS:  66.48999786376953   kJ/mol  BindingDB
RIT-TΔS:  50.27000045776367   kJ/mol  BindingDB
RITΔG:  42.63999938964844   kJ/mol  BindingDB
RITKi:  15   nM  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RITΔG:  43.470001220703125   kJ/mol  BindingDB
RIT-TΔS:  34.70000076293945   kJ/mol  BindingDB
RITKi:  23   nM  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RITΔH:  73.1500015258789   kJ/mol  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RITΔG:  38.040000915527344   kJ/mol  BindingDB
RITΔG:  31.770000457763672   kJ/mol  BindingDB
RITKd:  0.6000000238418579   nM  BindingDB
RITΔG:  57.68000030517578   kJ/mol  BindingDB
RIT-TΔS:  46.41999816894531   kJ/mol  BindingDB
RITKi:  60   nM  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RIT-TΔS:  58.560001373291016   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  69.83000183105469   kJ/mol  BindingDB
RITΔG:  53.91999816894531   kJ/mol  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RITΔG:  38.869998931884766   kJ/mol  BindingDB
RITKi:  0.46000000834465027   nM  BindingDB
RITΔH:  51   kJ/mol  BindingDB
RITΔG:  55.59000015258789   kJ/mol  BindingDB
RITΔG:  36.369998931884766   kJ/mol  BindingDB
RITKi:  0.029999999329447746   nM  BindingDB
RIT-TΔS:  44.75   kJ/mol  BindingDB
RITΔG:  57.27000045776367   kJ/mol  BindingDB
RITΔG:  34.279998779296875   kJ/mol  BindingDB
RITΔH:  11.699999809265137   kJ/mol  BindingDB
RITΔG:  36.779998779296875   kJ/mol  BindingDB
RITKi:  2.4000000953674316   nM  BindingDB
RITΔH:  25.079999923706055   kJ/mol  BindingDB
RITΔH:  27.59000015258789   kJ/mol  BindingDB
RIT-TΔS:  70.2699966430664   kJ/mol  BindingDB
RITΔH:  0.07999999821186066   kJ/mol  BindingDB
RIT-TΔS:  102.05999755859375   kJ/mol  BindingDB
RITKi:  109   nM  BindingDB
RITKi:  13   nM  BindingDB
RITΔH:  22.56999969482422   kJ/mol  BindingDB
RIT-TΔS:  57.29999923706055   kJ/mol  BindingDB
RITΔG:  33.439998626708984   kJ/mol  BindingDB
RITΔH:  26.75   kJ/mol  BindingDB
RITΔH:  24.239999771118164   kJ/mol  BindingDB
RITΔG:  50.15999984741211   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RITKi:  0.3700000047683716   nM  BindingDB
RITΔG:  54.34000015258789   kJ/mol  BindingDB
RITΔH:  2.0899999141693115   kJ/mol  BindingDB
RITΔH:  33.439998626708984   kJ/mol  BindingDB
RITKi:  0.9100000262260437   nM  BindingDB
RITΔG:  41.79999923706055   kJ/mol  BindingDB
RITΔG:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  51.0099983215332   kJ/mol  BindingDB
RITΔH:  17.969999313354492   kJ/mol  BindingDB
RIT-TΔS:  42.25   kJ/mol  BindingDB
RIT-TΔS:  70.2699966430664   kJ/mol  BindingDB
RITKi:  30   nM  BindingDB
RITΔH:  3.759999990463257   kJ/mol  BindingDB
RIT-TΔS:  57.33000183105469   kJ/mol  BindingDB
RITΔH:  9.609999656677246   kJ/mol  BindingDB
RITΔG:  44.72999954223633   kJ/mol  BindingDB
RITKi:  2.809999942779541   nM  BindingDB
RITΔG:  60.189998626708984   kJ/mol  BindingDB
RITKi:  0.15000000596046448   nM  BindingDB
RITΔH:  43.470001220703125   kJ/mol  BindingDB
RIT-TΔS:  82.80000305175781   kJ/mol  BindingDB
RIT-TΔS:  33.040000915527344   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
BRITONAVIRPeptide-like /  Inhibitor


Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.121α = 90
b = 62.121β = 90
c = 84.784γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
Omodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    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