The HIV protease (mutant Q7K L33I L63I V82F I84V) complexed with KNI-764 (an inhibitor)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease.

Vega, S.Kang, L.-W.Velazquez-Campoy, A.Kiso, Y.Amzel, L.M.Freire, E.

(2004) Proteins 55: 594-602

  • DOI: 10.1002/prot.20069
  • Primary Citation of Related Structures:  
    1MSN, 1MSM, 1MRX, 1MRW

  • PubMed Abstract: 
  • The efficacy of HIV-1 protease inhibition therapies is often compromised by the appearance of mutations in the protease molecule that lower the binding affinity of inhibitors while maintaining viable catalytic activity and substrate affinity. The V82 ...

    The efficacy of HIV-1 protease inhibition therapies is often compromised by the appearance of mutations in the protease molecule that lower the binding affinity of inhibitors while maintaining viable catalytic activity and substrate affinity. The V82F/I84V double mutation is located within the binding site cavity and affects all protease inhibitors in clinical use. KNI-764, a second-generation inhibitor currently under development, maintains significant potency against this mutation by entropically compensating for enthalpic losses, thus minimizing the loss in binding affinity. KNI-577 differs from KNI-764 by a single functional group critical to the inhibitor response to the protease mutation. This single difference changes the response of the two inhibitors to the mutation by one order of magnitude. Accordingly, a structural understanding of the inhibitor response will provide important guidelines for the design of inhibitors that are less susceptible to mutations conveying drug resistance. The structures of the two compounds bound to the wild type and V82F/I84V HIV-1 protease have been determined by X-ray crystallography at 2.0 A resolution. The presence of two asymmetric functional groups, linked by rotatable bonds to the inhibitor scaffold, allows KNI-764 to adapt to the mutated binding site cavity more readily than KNI-577, with a single asymmetric group. Both inhibitors lose about 2.5 kcal/mol in binding enthalpy when facing the drug-resistant mutant protease; however KNI-764 gains binding entropy while KNI-577 loses binding entropy. The gain in binding entropy by KNI-764 accounts for its low susceptibility to the drug-resistant mutation. The heat capacity change associated with binding becomes more negative when KNI-764 binds to the mutant protease, consistent with increased desolvation. With KNI-577, the opposite effect is observed. Structurally, the crystallographic B factors increase for KNI-764 when it is bound to the drug-resistant mutant. The opposite is observed for KNI-577. Consistent with these observations, it appears that KNI-764 is able to gain binding entropy by a two-fold mechanism: it gains solvation entropy by burying itself deeper within the binding pocket and gains conformational entropy by losing interaction with the protease.

    Organizational Affiliation

    Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL polyproteinAB99Human immunodeficiency virus 1Mutation(s): 5 
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 JE2

Download CCD File 
C32 H37 N3 O5 S
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JE2ΔH:  33.439998626708984   kJ/mol  BindingDB
JE2ΔG:  44.310001373291016   kJ/mol  BindingDB
JE2ΔH:  14.630000114440918   kJ/mol  BindingDB
JE2Ki:  0.3199999928474426   nM  BindingDB
JE2-TΔS:  59.38999938964844   kJ/mol  BindingDB
JE2ΔH:  25.079999923706055   kJ/mol  BindingDB
JE2ΔG:  51   kJ/mol  BindingDB
JE2ΔH:  16.299999237060547   kJ/mol  BindingDB
JE2ΔH:  15.050000190734863   kJ/mol  BindingDB
JE2ΔG:  49.31999969482422   kJ/mol  BindingDB
JE2ΔG:  60.61000061035156   kJ/mol  BindingDB
JE2-TΔS:  41   kJ/mol  BindingDB
JE2-TΔS:  62.310001373291016   kJ/mol  BindingDB
JE2-TΔS:  61.47999954223633   kJ/mol  BindingDB
JE2ΔH:  18.389999389648438   kJ/mol  BindingDB
JE2ΔH:  28.84000015258789   kJ/mol  BindingDB
JE2-TΔS:  61.900001525878906   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2-TΔS:  64.81999969482422   kJ/mol  BindingDB
JE2ΔH:  35.529998779296875   kJ/mol  BindingDB
JE2-TΔS:  51.0099983215332   kJ/mol  BindingDB
JE2ΔH:  14.210000038146973   kJ/mol  BindingDB
JE2ΔH:  10.869999885559082   kJ/mol  BindingDB
JE2-TΔS:  28.030000686645508   kJ/mol  BindingDB
JE2ΔH:  30.93000030517578   kJ/mol  BindingDB
JE2ΔH:  12.119999885559082   kJ/mol  BindingDB
JE2ΔH:  13.380000114440918   kJ/mol  BindingDB
JE2Ki:  0.1899999976158142   nM  BindingDB
JE2ΔG:  55.18000030517578   kJ/mol  BindingDB
JE2ΔG:  59.77000045776367   kJ/mol  BindingDB
JE2ΔG:  57.27000045776367   kJ/mol  BindingDB
JE2-TΔS:  35.119998931884766   kJ/mol  BindingDB
JE2Ki:  0.33000001311302185   nM  BindingDB
JE2ΔG:  54.34000015258789   kJ/mol  BindingDB
JE2-TΔS:  65.23999786376953   kJ/mol  BindingDB
JE2Ki:  0.07999999821186066   nM  BindingDB
JE2ΔG:  53.09000015258789   kJ/mol  BindingDB
JE2ΔG:  48.4900016784668   kJ/mol  BindingDB
JE2-TΔS:  44.75   kJ/mol  BindingDB
JE2-TΔS:  30.110000610351562   kJ/mol  BindingDB
JE2ΔH:  43.470001220703125   kJ/mol  BindingDB
JE2-TΔS:  30.530000686645508   kJ/mol  BindingDB
JE2ΔH:  8.779999732971191   kJ/mol  BindingDB
JE2-TΔS:  28.860000610351562   kJ/mol  BindingDB
JE2ΔH:  5.019999980926514   kJ/mol  BindingDB
JE2Ki:  0.550000011920929   nM  BindingDB
JE2ΔG:  51   kJ/mol  BindingDB
JE2ΔH:  8.359999656677246   kJ/mol  BindingDB
JE2-TΔS:  28.860000610351562   kJ/mol  BindingDB
JE2ΔG:  47.22999954223633   kJ/mol  BindingDB
JE2ΔG:  45.97999954223633   kJ/mol  BindingDB
JE2ΔG:  41.79999923706055   kJ/mol  BindingDB
JE2-TΔS:  71.11000061035156   kJ/mol  BindingDB
JE2-TΔS:  58.970001220703125   kJ/mol  BindingDB
JE2ΔG:  60.189998626708984   kJ/mol  BindingDB
JE2ΔG:  38.869998931884766   kJ/mol  BindingDB
JE2Ki:  0.03999999910593033   nM  BindingDB
JE2Ki:  5.599999904632568   nM  BindingDB
JE2ΔH:  31.770000457763672   kJ/mol  BindingDB
JE2-TΔS:  26.360000610351562   kJ/mol  BindingDB
JE2Ki:  0.10999999940395355   nM  BindingDB
JE2-TΔS:  33.040000915527344   kJ/mol  BindingDB
JE2-TΔS:  30.110000610351562   kJ/mol  BindingDB
JE2-TΔS:  60.22999954223633   kJ/mol  BindingDB
JE2ΔG:  40.54999923706055   kJ/mol  BindingDB
JE2ΔH:  27.59000015258789   kJ/mol  BindingDB
JE2Ki:  0.10999999940395355   nM  BindingDB
JE2ΔG:  50.15999984741211   kJ/mol  BindingDB
JE2ΔH:  27.59000015258789   kJ/mol  BindingDB
JE2ΔG:  54.7599983215332   kJ/mol  BindingDB
JE2-TΔS:  43.91999816894531   kJ/mol  BindingDB
JE2-TΔS:  102.05999755859375   kJ/mol  BindingDB
JE2ΔH:  25.5   kJ/mol  BindingDB
K64Kd :  0.8100000023841858   nM  PDBBind
JE2Kd:  81   nM  Binding MOAD
JE2-TΔS:  34.290000915527344   kJ/mol  BindingDB
JE2Ki:  9.399999618530273   nM  BindingDB
JE2ΔG:  62.279998779296875   kJ/mol  BindingDB
JE2ΔG:  53.09000015258789   kJ/mol  BindingDB
JE2ΔH:  13.789999961853027   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2ΔH:  7.940000057220459   kJ/mol  BindingDB
JE2ΔG:  51.83000183105469   kJ/mol  BindingDB
JE2ΔH:  6.690000057220459   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2Ki:  0.029999999329447746   nM  BindingDB
JE2-TΔS:  65.23999786376953   kJ/mol  BindingDB
JE2-TΔS:  57.29999923706055   kJ/mol  BindingDB
JE2ΔG:  49.7400016784668   kJ/mol  BindingDB
JE2-TΔS:  30.950000762939453   kJ/mol  BindingDB
JE2ΔH:  24.239999771118164   kJ/mol  BindingDB
JE2ΔH:  21.31999969482422   kJ/mol  BindingDB
JE2ΔH:  31.350000381469727   kJ/mol  BindingDB
JE2ΔG:  55.18000030517578   kJ/mol  BindingDB
JE2ΔH:  14.630000114440918   kJ/mol  BindingDB
JE2-TΔS:  77.37000274658203   kJ/mol  BindingDB
JE2ΔH:  73.1500015258789   kJ/mol  BindingDB
JE2-TΔS:  59.810001373291016   kJ/mol  BindingDB
JE2-TΔS:  65.6500015258789   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2ΔG:  62.279998779296875   kJ/mol  BindingDB
JE2ΔG:  53.5   kJ/mol  BindingDB
JE2ΔG:  52.25   kJ/mol  BindingDB
JE2ΔH:  15.470000267028809   kJ/mol  BindingDB
JE2-TΔS:  64.81999969482422   kJ/mol  BindingDB
JE2ΔG:  35.529998779296875   kJ/mol  BindingDB
JE2ΔH:  0   kJ/mol  BindingDB
JE2ΔG:  42.63999938964844   kJ/mol  BindingDB
JE2ΔG:  57.68000030517578   kJ/mol  BindingDB
JE2ΔH:  15.470000267028809   kJ/mol  BindingDB
JE2ΔG:  62.279998779296875   kJ/mol  BindingDB
JE2ΔG:  28.84000015258789   kJ/mol  BindingDB
JE2ΔH:  12.119999885559082   kJ/mol  BindingDB
JE2ΔH:  9.199999809265137   kJ/mol  BindingDB
JE2ΔH:  25.079999923706055   kJ/mol  BindingDB
JE2ΔH:  18.389999389648438   kJ/mol  BindingDB
JE2-TΔS:  43.08000183105469   kJ/mol  BindingDB
JE2-TΔS:  65.6500015258789   kJ/mol  BindingDB
JE2-TΔS:  28.030000686645508   kJ/mol  BindingDB
JE2ΔG:  53.91999816894531   kJ/mol  BindingDB
JE2-TΔS:  79.04000091552734   kJ/mol  BindingDB
JE2ΔG:  61.45000076293945   kJ/mol  BindingDB
JE2-TΔS:  65.6500015258789   kJ/mol  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000566 (JE2)
Query on PRD_000566
BKNI-764Peptide-like /  Enzyme inhibitor


Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.484α = 90
b = 86.302β = 90
c = 46.14γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    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: 2012-12-12
    Changes: Other