Crystal structure of HIV-1 mutant I50V and inhibitor saquinavira

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.

Liu, F.Kovalevsky, A.Y.Tie, Y.Ghosh, A.K.Harrison, R.W.Weber, I.T.

(2008) J Mol Biol 381: 102-115

  • DOI: 10.1016/j.jmb.2008.05.062
  • Primary Citation of Related Structures:  
    3D1X, 3D1Y, 3D1Z, 3D20, 3CYW, 3CYX

  • PubMed Abstract: 
  • HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently c ...

    HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistant HIV. Structural and kinetic analyses were used to investigate the role of flap residues Gly48, Ile50, and Ile54 in the development of drug resistance. The crystal structures of flap mutants PR(I50V) (PR with I50V mutation), PR(I54V) (PR with I54V mutation), and PR(I54M) (PR with I54M mutation) complexed with saquinavir (SQV) as well as PR(G48V) (PR with G48V mutation), PR(I54V), and PR(I54M) complexed with darunavir (DRV) were determined at resolutions of 1.05-1.40 A. The PR mutants showed changes in flap conformation, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type PR. The PR contacts with DRV were closer in PR(G48V)-DRV than in the wild-type PR-DRV, whereas they were longer in PR(I54M)-DRV. The relative inhibition of PR(I54V) and that of PR(I54M) were similar for SQV and DRV. PR(G48V) was about twofold less susceptible to SQV than to DRV, whereas the opposite was observed for PR(I50V). The observed inhibition was in agreement with the association of G48V and I50V with clinical resistance to SQV and DRV, respectively. This analysis of structural and kinetic effects of the mutants will assist in the development of more effective inhibitors for drug-resistant HIV.

    Related Citations: 
    • Ultra-High Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor Tmc114
      Kovalevsky, A.Y., Liu, F., Leshchenko, S., Ghosh, A.K., Harrison, R.W., Weber, I.T.
      (2006) J Mol Biol 365: 901
    • Kinetic, Stability, and Structural Changes in High-Resolution Crystal Structures of HIV-1 Protease with Drug-Resistant Mutations L24I, I50V, and G73S.
      Liu, F., Boross, P.I., Wang, Y.F., Tozser, J., Louis, J.M., Harrison, R.W., Weber, I.T.
      (2005) J Mol Biol 354: 789

    Organizational Affiliation

    Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 ProteaseAB99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag-pol
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Explore P04587 
Go to UniProtKB:  P04587
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on ROC

Download CCD File 
(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
 Ligand Interaction
Query on PO4

Download CCD File 
O4 P
 Ligand Interaction
Query on GOL

Download CCD File 
C3 H8 O3
 Ligand Interaction
Query on ACY

Download CCD File 
C2 H4 O2
 Ligand Interaction
Query on NA

Download CCD File 
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ROCIC50:  30   nM  BindingDB
ROCΔG:  51.83000183105469   kJ/mol  BindingDB
ROCΔG:  50.58000183105469   kJ/mol  BindingDB
ROCΔH:  15.050000190734863   kJ/mol  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCΔH:  3.759999990463257   kJ/mol  BindingDB
ROCΔG:  60.61000061035156   kJ/mol  BindingDB
ROCΔH:  22.56999969482422   kJ/mol  BindingDB
ROCΔG:  50.15999984741211   kJ/mol  BindingDB
ROCΔG:  41.79999923706055   kJ/mol  BindingDB
ROCΔG:  35.529998779296875   kJ/mol  BindingDB
ROCΔG:  57.68000030517578   kJ/mol  BindingDB
ROCΔG:  51.40999984741211   kJ/mol  BindingDB
ROCKi:  0.20000000298023224   nM  BindingDB
ROC-TΔS:  61.47999954223633   kJ/mol  BindingDB
ROC-TΔS:  80.29000091552734   kJ/mol  BindingDB
ROC-TΔS:  79.04000091552734   kJ/mol  BindingDB
ROCΔG:  44.310001373291016   kJ/mol  BindingDB
ROC-TΔS:  59.38999938964844   kJ/mol  BindingDB
ROCΔH:  40.130001068115234   kJ/mol  BindingDB
ROC-TΔS:  55.630001068115234   kJ/mol  BindingDB
ROCΔH:  6.690000057220459   kJ/mol  BindingDB
ROC-TΔS:  60.63999938964844   kJ/mol  BindingDB
ROCKi:  0.6499999761581421   nM  BindingDB
ROCIC50:  1.7999999523162842   nM  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCKi :  10   nM  PDBBind
ROCIC50:  45   nM  BindingDB
ROCΔH:  14.630000114440918   kJ/mol  BindingDB
ROC-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROCΔG:  49.31999969482422   kJ/mol  BindingDB
ROCKi:  0.8999999761581421   nM  BindingDB
ROCΔG:  36.779998779296875   kJ/mol  BindingDB
ROC-TΔS:  71.5   kJ/mol  BindingDB
ROCKd:  0.5799999833106995   nM  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROC-TΔS:  75.27999877929688   kJ/mol  BindingDB
ROCKi:  3.700000047683716   nM  BindingDB
ROCKi:  1.2999999523162842   nM  BindingDB
ROCIC50:  0.20000000298023224   nM  BindingDB
ROCIC50:  0.23000000417232513   nM  BindingDB
ROCIC50:  270   nM  BindingDB
ROCΔH:  2.0899999141693115   kJ/mol  BindingDB
ROCKi:  15   nM  BindingDB
ROCKi:  78.44000244140625   nM  BindingDB
ROCIC50:  0.3400000035762787   nM  BindingDB
ROCIC50:  8.399999618530273   nM  BindingDB
ROCΔG:  62.279998779296875   kJ/mol  BindingDB
ROCΔH:  31.770000457763672   kJ/mol  BindingDB
ROCΔH:  26.75   kJ/mol  BindingDB
ROCKi:  0.44999998807907104   nM  BindingDB
ROC-TΔS:  41   kJ/mol  BindingDB
ROCΔH:  15.470000267028809   kJ/mol  BindingDB
ROC-TΔS:  33.040000915527344   kJ/mol  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCKi:  0.46000000834465027   nM  BindingDB
ROC-TΔS:  28.030000686645508   kJ/mol  BindingDB
ROCIC50:  16   nM  BindingDB
ROCΔH:  35.529998779296875   kJ/mol  BindingDB
ROCΔG:  43.470001220703125   kJ/mol  BindingDB
ROC-TΔS:  30.530000686645508   kJ/mol  BindingDB
ROCΔH:  21.31999969482422   kJ/mol  BindingDB
ROCΔG:  61.45000076293945   kJ/mol  BindingDB
ROCKi:  1.399999976158142   nM  BindingDB
ROCKi:  138   nM  BindingDB
ROC-TΔS:  65.6500015258789   kJ/mol  BindingDB
ROCΔH:  12.539999961853027   kJ/mol  BindingDB
ROCΔG:  56.43000030517578   kJ/mol  BindingDB
ROCKi:  0.03999999910593033   nM  BindingDB
ROCΔG:  38.040000915527344   kJ/mol  BindingDB
ROC-TΔS:  43.91999816894531   kJ/mol  BindingDB
ROC-TΔS:  46.41999816894531   kJ/mol  BindingDB
ROC-TΔS:  61.45000076293945   kJ/mol  BindingDB
ROC-TΔS:  65.6500015258789   kJ/mol  BindingDB
ROCΔG:  42.63999938964844   kJ/mol  BindingDB
ROCΔH:  18.389999389648438   kJ/mol  BindingDB
ROCΔG:  47.650001525878906   kJ/mol  BindingDB
ROCKi:  117   nM  BindingDB
ROC-TΔS:  76.94999694824219   kJ/mol  BindingDB
ROC-TΔS:  64.81999969482422   kJ/mol  BindingDB
ROCΔG:  43.470001220703125   kJ/mol  BindingDB
ROC-TΔS:  60.22999954223633   kJ/mol  BindingDB
ROCIC50:  1.7000000476837158   nM  BindingDB
ROCIC50:  11   nM  BindingDB
ROCΔH:  40.130001068115234   kJ/mol  BindingDB
ROCKi:  0.23000000417232513   nM  BindingDB
ROCΔG:  52.25   kJ/mol  BindingDB
ROC-TΔS:  43.91999816894531   kJ/mol  BindingDB
ROCΔH:  16.299999237060547   kJ/mol  BindingDB
ROCKi:  89.52999877929688   nM  BindingDB
ROC-TΔS:  59.810001373291016   kJ/mol  BindingDB
ROC-TΔS:  77.37000274658203   kJ/mol  BindingDB
ROC-TΔS:  61.900001525878906   kJ/mol  BindingDB
ROCIC50:  11.199999809265137   nM  BindingDB
ROC-TΔS:  50.27000045776367   kJ/mol  BindingDB
ROC-TΔS:  33.040000915527344   kJ/mol  BindingDB
ROCΔG:  52.66999816894531   kJ/mol  BindingDB
ROC-TΔS:  58.59000015258789   kJ/mol  BindingDB
ROC-TΔS:  58.13999938964844   kJ/mol  BindingDB
ROC-TΔS:  30.110000610351562   kJ/mol  BindingDB
ROCΔH:  11.699999809265137   kJ/mol  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCΔH:  9.199999809265137   kJ/mol  BindingDB
ROCΔG:  54.7599983215332   kJ/mol  BindingDB
ROC-TΔS:  46.84000015258789   kJ/mol  BindingDB
ROCΔH:  12.119999885559082   kJ/mol  BindingDB
ROCΔG:  50.15999984741211   kJ/mol  BindingDB
ROCΔG:  38.869998931884766   kJ/mol  BindingDB
ROCΔH:  9.609999656677246   kJ/mol  BindingDB
ROCKi:  0.25   nM  BindingDB
ROCΔH:  8.779999732971191   kJ/mol  BindingDB
ROCΔG:  49.31999969482422   kJ/mol  BindingDB
ROCΔH:  27.59000015258789   kJ/mol  BindingDB
ROCΔH:  25.5   kJ/mol  BindingDB
ROCΔH:  10.029999732971191   kJ/mol  BindingDB
ROC-TΔS:  44.75   kJ/mol  BindingDB
ROC-TΔS:  57.29999923706055   kJ/mol  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCΔH:  15.470000267028809   kJ/mol  BindingDB
ROC-TΔS:  74.02999877929688   kJ/mol  BindingDB
ROCKi:  0.03999999910593033   nM  BindingDB
ROCKi:  0.41999998688697815   nM  BindingDB
ROCΔG:  51   kJ/mol  BindingDB
ROCΔG:  55.18000030517578   kJ/mol  BindingDB
ROCΔH:  25.079999923706055   kJ/mol  BindingDB
ROCKd:  0.6399999856948853   nM  BindingDB
ROCΔG:  41.79999923706055   kJ/mol  BindingDB
ROCIC50:  1   nM  BindingDB
ROC-TΔS:  71.11000061035156   kJ/mol  BindingDB
ROCΔH:  9.199999809265137   kJ/mol  BindingDB
ROCKi:  0.1899999976158142   nM  BindingDB
ROCΔH:  12.119999885559082   kJ/mol  BindingDB
ROCΔG:  60.189998626708984   kJ/mol  BindingDB
ROC-TΔS:  43.08000183105469   kJ/mol  BindingDB
ROCKd:  0.3100000023841858   nM  BindingDB
ROCKi:  0.5199999809265137   nM  BindingDB
ROC-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROCKd:  4.099999904632568   nM  BindingDB
ROC-TΔS:  35.119998931884766   kJ/mol  BindingDB
ROC-TΔS:  64.81999969482422   kJ/mol  BindingDB
ROCKi:  2   nM  BindingDB
ROCΔH:  14.630000114440918   kJ/mol  BindingDB
ROCΔG:  53.09000015258789   kJ/mol  BindingDB
ROCΔH:  13.789999961853027   kJ/mol  BindingDB
ROCΔG:  40.130001068115234   kJ/mol  BindingDB
ROCΔG:  59.77000045776367   kJ/mol  BindingDB
ROC-TΔS:  56.86000061035156   kJ/mol  BindingDB
ROCΔG:  49.7400016784668   kJ/mol  BindingDB
ROC-TΔS:  70.2699966430664   kJ/mol  BindingDB
ROCΔH:  7.940000057220459   kJ/mol  BindingDB
ROCΔG:  47.22999954223633   kJ/mol  BindingDB
ROCΔG:  45.97999954223633   kJ/mol  BindingDB
ROC-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROCKi:  0.11999999731779099   nM  BindingDB
ROCΔG:  55.59000015258789   kJ/mol  BindingDB
ROCΔG:  54.34000015258789   kJ/mol  BindingDB
ROCΔH:  30.93000030517578   kJ/mol  BindingDB
ROCΔH:  12.960000038146973   kJ/mol  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCΔH:  0.07999999821186066   kJ/mol  BindingDB
ROCΔH:  8.779999732971191   kJ/mol  BindingDB
ROCΔH:  35.11000061035156   kJ/mol  BindingDB
ROCKi:  0.05999999865889549   nM  BindingDB
ROCΔH:  20.059999465942383   kJ/mol  BindingDB
ROCΔH:  12.539999961853027   kJ/mol  BindingDB
ROCΔH:  17.969999313354492   kJ/mol  BindingDB
ROCKi:  10   nM  Binding MOAD
ROCKd:  0.3199999928474426   nM  BindingDB
ROC-TΔS:  66.48999786376953   kJ/mol  BindingDB
ROCKi:  1.7999999523162842   nM  BindingDB
ROCΔH:  10.869999885559082   kJ/mol  BindingDB
ROCΔG:  47.22999954223633   kJ/mol  BindingDB
ROCΔH:  11.699999809265137   kJ/mol  BindingDB
ROC-TΔS:  61.900001525878906   kJ/mol  BindingDB
ROC-TΔS:  57.33000183105469   kJ/mol  BindingDB
ROCΔH:  5.019999980926514   kJ/mol  BindingDB
ROCΔG:  57.27000045776367   kJ/mol  BindingDB
ROCΔH:  8.359999656677246   kJ/mol  BindingDB
ROCΔH:  43.470001220703125   kJ/mol  BindingDB
ROCKi:  1.0299999713897705   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
ASaquinavirPeptide-like /  Inhibitor


Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.9α = 90
b = 86.02β = 90
c = 46.39γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Deposited Date: 2008-04-27 
  • Released Date: 2008-05-27 
  • Deposition Author(s): Liu, F., Weber, I.T.

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Other