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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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 of active- and nonactive-site mutations to the resistance ...

    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 polyproteinA, B99Human 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 MK1

Download Ideal Coordinates CCD File 
C36 H47 N5 O4
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MK1-TΔS:  65.23999786376953   kJ/mol  BindingDB
MK1Ki:  0.36000001430511475   nM  BindingDB
MK1Ki:  2.640000104904175   nM  BindingDB
MK1ΔG:  62.279998779296875   kJ/mol  BindingDB
MK1Ki:  0.3799999952316284   nM  BindingDB
MK1-TΔS:  65.68000030517578   kJ/mol  BindingDB
MK1Ki:  3.0999999046325684   nM  BindingDB
MK1ΔG:  58.099998474121094   kJ/mol  BindingDB
MK1ΔH:  17.969999313354492   kJ/mol  BindingDB
MK1IC50:  0.36000001430511475   nM  BindingDB
MK1-TΔS:  55.630001068115234   kJ/mol  BindingDB
MK1ΔH:  6.690000057220459   kJ/mol  BindingDB
MK1Ki:  69   nM  BindingDB
MK1ΔH:  10.869999885559082   kJ/mol  BindingDB
MK1IC50:  0.6000000238418579   nM  BindingDB
MK1ΔG:  51   kJ/mol  BindingDB
MK1-TΔS:  65.6500015258789   kJ/mol  BindingDB
MK1-TΔS:  47.2599983215332   kJ/mol  BindingDB
MK1Ki:  0.3700000047683716   nM  BindingDB
MK1Ki:  62   nM  BindingDB
MK1ΔH:  33.439998626708984   kJ/mol  BindingDB
MK1ΔH:  11.699999809265137   kJ/mol  BindingDB
MK1-TΔS:  62.310001373291016   kJ/mol  BindingDB
MK1ΔG:  53.5   kJ/mol  BindingDB
MK1ΔH:  8.779999732971191   kJ/mol  BindingDB
MK1ΔH:  11.699999809265137   kJ/mol  BindingDB
MK1ΔG:  43.470001220703125   kJ/mol  BindingDB
MK1ΔH:  9.199999809265137   kJ/mol  BindingDB
MK1IC50:  0.5899999737739563   nM  BindingDB
MK1-TΔS:  70.2699966430664   kJ/mol  BindingDB
MK1ΔH:  18.389999389648438   kJ/mol  BindingDB
MK1ΔH:  35.11000061035156   kJ/mol  BindingDB
MK1-TΔS:  61.900001525878906   kJ/mol  BindingDB
MK1IC50:  89   nM  BindingDB
MK1ΔH:  24.65999984741211   kJ/mol  BindingDB
MK1-TΔS:  71.5   kJ/mol  BindingDB
MK1Ki:  2.809999942779541   nM  BindingDB
MK1ΔH:  27.59000015258789   kJ/mol  BindingDB
MK1IC50:  0.5600000023841858   nM  BindingDB
MK1Ki:  2   nM  BindingDB
MK1IC50:  44   nM  BindingDB
MK1ΔH:  31.770000457763672   kJ/mol  BindingDB
MK1ΔG:  38.869998931884766   kJ/mol  BindingDB
MK1-TΔS:  58.13999938964844   kJ/mol  BindingDB
MK1Ki:  0.3100000023841858   nM  BindingDB
MK1IC50:  0.4099999964237213   nM  BindingDB
MK1IC50:  52   nM  BindingDB
MK1IC50:  56   nM  BindingDB
MK1ΔH:  8.779999732971191   kJ/mol  BindingDB
MK1-TΔS:  28.860000610351562   kJ/mol  BindingDB
MK1IC50:  61   nM  BindingDB
MK1IC50:  1.600000023841858   nM  BindingDB
MK1Ki:  0.5400000214576721   nM  BindingDB
MK1ΔG:  51.40999984741211   kJ/mol  BindingDB
MK1ΔH:  26.75   kJ/mol  BindingDB
MK1Ki:  3.0999999046325684   nM  BindingDB
MK1Ki:  0.10999999940395355   nM  BindingDB
MK1Ki:  4.400000095367432   nM  BindingDB
MK1IC50:  370   nM  BindingDB
MK1-TΔS:  30.110000610351562   kJ/mol  BindingDB
MK1Ki:  1.340000033378601   nM  BindingDB
MK1ΔG:  54.7599983215332   kJ/mol  BindingDB
MK1Ki:  0.3199999928474426   nM  BindingDB
MK1ΔG:  40.54999923706055   kJ/mol  BindingDB
MK1ΔG:  47.22999954223633   kJ/mol  BindingDB
MK1-TΔS:  44.75   kJ/mol  BindingDB
MK1Ki:  0.5199999809265137   nM  BindingDB
MK1Ki :  4235   nM  PDBBind
MK1ΔG:  60.189998626708984   kJ/mol  BindingDB
MK1-TΔS:  59.38999938964844   kJ/mol  BindingDB
MK1ΔG:  63.119998931884766   kJ/mol  BindingDB
MK1ΔH:  0   kJ/mol  BindingDB
MK1Ki:  0.05000000074505806   nM  BindingDB
MK1Ki:  3.109999895095825   nM  BindingDB
MK1-TΔS:  60.63999938964844   kJ/mol  BindingDB
MK1ΔG:  51.83000183105469   kJ/mol  BindingDB
MK1Ki:  289   nM  BindingDB
MK1Ki:  2.700000047683716   nM  BindingDB
MK1-TΔS:  58.970001220703125   kJ/mol  BindingDB
MK1-TΔS:  74.02999877929688   kJ/mol  BindingDB
MK1ΔG:  49.7400016784668   kJ/mol  BindingDB
MK1ΔG:  47.650001525878906   kJ/mol  BindingDB
MK1Ki:  5.099999904632568   nM  BindingDB
MK1Ki:  2.799999952316284   nM  BindingDB
MK1Ki:  0.800000011920929   nM  BindingDB
MK1Kd:  1.0700000524520874   nM  BindingDB
MK1Ki:  2.509999990463257   nM  BindingDB
MK1IC50:  35   nM  BindingDB
MK1Ki:  6.619999885559082   nM  BindingDB
MK1ΔH:  20.059999465942383   kJ/mol  BindingDB
MK1-TΔS:  63.150001525878906   kJ/mol  BindingDB
MK1-TΔS:  61.900001525878906   kJ/mol  BindingDB
MK1ΔH:  16.299999237060547   kJ/mol  BindingDB
MK1ΔG:  54.34000015258789   kJ/mol  BindingDB
MK1ΔG:  53.09000015258789   kJ/mol  BindingDB
MK1ΔG:  43.470001220703125   kJ/mol  BindingDB
MK1Ki:  7.599999904632568   nM  BindingDB
MK1ΔG:  59.77000045776367   kJ/mol  BindingDB
MK1IC50:  0.5899999737739563   nM  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1Ki:  4235   nM  Binding MOAD
MK1ΔH:  15.470000267028809   kJ/mol  BindingDB
MK1ΔG:  53.5   kJ/mol  BindingDB
MK1ΔH:  5.019999980926514   kJ/mol  BindingDB
MK1ΔH:  7.940000057220459   kJ/mol  BindingDB
MK1IC50:  61.20000076293945   nM  BindingDB
MK1ΔH:  7.519999980926514   kJ/mol  BindingDB
MK1-TΔS:  49.34000015258789   kJ/mol  BindingDB
MK1IC50:  0.6000000238418579   nM  BindingDB
MK1ΔG:  57.68000030517578   kJ/mol  BindingDB
MK1IC50:  0.36000001430511475   nM  BindingDB
MK1-TΔS:  28.030000686645508   kJ/mol  BindingDB
MK1ΔH:  12.539999961853027   kJ/mol  BindingDB
MK1-TΔS:  57.29999923706055   kJ/mol  BindingDB
MK1IC50:  20.100000381469727   nM  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1-TΔS:  65.6500015258789   kJ/mol  BindingDB
MK1-TΔS:  61.45000076293945   kJ/mol  BindingDB
MK1Ki:  0.2800000011920929   nM  BindingDB
MK1ΔH:  15.470000267028809   kJ/mol  BindingDB
MK1-TΔS:  64.81999969482422   kJ/mol  BindingDB
MK1Ki:  0.23999999463558197   nM  BindingDB
MK1Ki:  12   nM  BindingDB
MK1Ki:  40   nM  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1Ki:  50   nM  BindingDB
MK1Ki:  398   nM  BindingDB
MK1ΔG:  42.63999938964844   kJ/mol  BindingDB
MK1-TΔS:  58.59000015258789   kJ/mol  BindingDB
MK1Ki:  0.5799999833106995   nM  BindingDB
MK1ΔH:  15.050000190734863   kJ/mol  BindingDB
MK1Ki:  15   nM  BindingDB
MK1ΔG:  45.13999938964844   kJ/mol  BindingDB
MK1-TΔS:  64.81999969482422   kJ/mol  BindingDB
MK1ΔG:  62.279998779296875   kJ/mol  BindingDB
MK1ΔG:  38.459999084472656   kJ/mol  BindingDB
MK1ΔH:  15.880000114440918   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.573α = 90
b = 61.574β = 90
c = 84.109γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
Omodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation