Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High Resolution X-ray Crystallography

Experimental Data Snapshot

  • Resolution: 0.93 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.104 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography.

Adachi, M.Ohhara, T.Kurihara, K.Tamada, T.Honjo, E.Okazaki, N.Arai, S.Shoyama, Y.Kimura, K.Matsumura, H.Sugiyama, S.Adachi, H.Takano, K.Mori, Y.Hidaka, K.Kimura, T.Hayashi, Y.Kiso, Y.Kuroki, R.

(2009) Proc Natl Acad Sci U S A 

  • DOI: 10.1073/pnas.0809400106
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • HIV-1 protease is a dimeric aspartic protease that plays an essential role in viral replication. To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in th ...

    HIV-1 protease is a dimeric aspartic protease that plays an essential role in viral replication. To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp-25 and Asp-125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9-A resolution and X-ray crystallography at 1.4-A resolution. The resulting structural data show that the catalytic residue Asp-25 is protonated and that Asp-125 (the catalytic residue from the corresponding diad-related molecule) is deprotonated. The proton on Asp-25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine (Apns) group in KNI-272. The deprotonated Asp-125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.

    Organizational Affiliation

    Molecular Structural Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
proteaseA, B99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on KNI

Download CCD File 
C33 H41 N5 O6 S2
 Ligand Interaction
Query on GOL

Download CCD File 
A, B
C3 H8 O3
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000562 (KNI)
Query on PRD_000562
Bkynostatin 272P /  Enzyme inhibitor


External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KNI-TΔS:  46.84000015258789   kJ/mol  BindingDB
KNIΔG:  62.279998779296875   kJ/mol  BindingDB
KNI-TΔS:  80.29000091552734   kJ/mol  BindingDB
KNIΔH:  10.869999885559082   kJ/mol  BindingDB
KNIΔG:  56.0099983215332   kJ/mol  BindingDB
KNI-TΔS:  70.66000366210938   kJ/mol  BindingDB
KNI-TΔS:  60.63999938964844   kJ/mol  BindingDB
KNIΔG:  45.97999954223633   kJ/mol  BindingDB
KNIΔH:  8.779999732971191   kJ/mol  BindingDB
KNIKi:  0.009999999776482582   nM  BindingDB
KNIKi:  0.8999999761581421   nM  BindingDB
KNIΔH:  12.539999961853027   kJ/mol  BindingDB
KNIΔG:  54.34000015258789   kJ/mol  BindingDB
KNIΔG:  50.15999984741211   kJ/mol  BindingDB
KNIKi:  0.6000000238418579   nM  BindingDB
KNIΔG:  52.25   kJ/mol  BindingDB
KNIΔH:  13.380000114440918   kJ/mol  BindingDB
KNI-TΔS:  64.81999969482422   kJ/mol  BindingDB
KNIΔG:  51.83000183105469   kJ/mol  BindingDB
KNIKi:  0.7400000095367432   nM  BindingDB
KNIΔH:  14.210000038146973   kJ/mol  BindingDB
KNIΔH:  0   kJ/mol  BindingDB
KNIΔG:  53.91999816894531   kJ/mol  BindingDB
KNIΔG:  48.4900016784668   kJ/mol  BindingDB
KNI-TΔS:  59.38999938964844   kJ/mol  BindingDB
KNIΔH:  40.130001068115234   kJ/mol  BindingDB
KNI-TΔS:  65.23999786376953   kJ/mol  BindingDB
KNIΔG:  50.58000183105469   kJ/mol  BindingDB
KNIΔG:  45.560001373291016   kJ/mol  BindingDB
KNIΔH:  31.350000381469727   kJ/mol  BindingDB
KNI-TΔS:  43.91999816894531   kJ/mol  BindingDB
KNI-TΔS:  30.950000762939453   kJ/mol  BindingDB
KNIKi:  0.3700000047683716   nM  BindingDB
KNIΔH:  22.56999969482422   kJ/mol  BindingDB
KNIΔH:  12.119999885559082   kJ/mol  BindingDB
KNIΔH:  20.059999465942383   kJ/mol  BindingDB
KNIΔH:  12.960000038146973   kJ/mol  BindingDB
KNIΔH:  0.07999999821186066   kJ/mol  BindingDB
KNI-TΔS:  64.81999969482422   kJ/mol  BindingDB
KNIΔH:  8.359999656677246   kJ/mol  BindingDB
KNI-TΔS:  66.48999786376953   kJ/mol  BindingDB
KNI-TΔS:  75.27999877929688   kJ/mol  BindingDB
KNIΔG:  40.130001068115234   kJ/mol  BindingDB
KNI-TΔS:  46.41999816894531   kJ/mol  BindingDB
KNIΔH:  21.739999771118164   kJ/mol  BindingDB
KNIKi:  1   nM  Binding MOAD
KNIΔG:  38.040000915527344   kJ/mol  BindingDB
KNIΔH:  27.170000076293945   kJ/mol  BindingDB
KNI-TΔS:  43.08000183105469   kJ/mol  BindingDB
KNIΔG:  48.4900016784668   kJ/mol  BindingDB
KNIKi:  1.100000023841858   nM  BindingDB
KNI-TΔS:  42.25   kJ/mol  BindingDB
KNIKi:  0.5799999833106995   nM  BindingDB
KNI-TΔS:  33.040000915527344   kJ/mol  BindingDB
KNIΔG:  56.43000030517578   kJ/mol  BindingDB
KNIΔH:  25.079999923706055   kJ/mol  BindingDB
KNI-TΔS:  32.20000076293945   kJ/mol  BindingDB
KNIΔG:  55.59000015258789   kJ/mol  BindingDB
KNIΔH:  9.609999656677246   kJ/mol  BindingDB
KNIKi:  0.3799999952316284   nM  BindingDB
KNIΔG:  53.5   kJ/mol  BindingDB
KNI-TΔS:  76.54000091552734   kJ/mol  BindingDB
KNIΔH:  12.119999885559082   kJ/mol  BindingDB
KNIΔH:  12.960000038146973   kJ/mol  BindingDB
KNIΔG:  51.83000183105469   kJ/mol  BindingDB
KNIΔH:  30.510000228881836   kJ/mol  BindingDB
KNIΔG:  52.66999816894531   kJ/mol  BindingDB
KNI-TΔS:  50.27000045776367   kJ/mol  BindingDB
KNIKi:  1.7000000476837158   nM  BindingDB
KNI-TΔS:  79.04000091552734   kJ/mol  BindingDB
KNI-TΔS:  45.59000015258789   kJ/mol  BindingDB
KNIΔG:  41.79999923706055   kJ/mol  BindingDB
KNIΔH:  2.0899999141693115   kJ/mol  BindingDB
KNIKi:  1.7000000476837158   nM  BindingDB
KNI-TΔS:  34.290000915527344   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Resolution: 0.93 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.104 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.532α = 90
b = 85.955β = 90
c = 46.386γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    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: 2012-12-12
    Changes: Other