Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine.

Baldwin, E.T.Bhat, T.N.Gulnik, S.Liu, B.Topol, I.A.Kiso, Y.Mimoto, T.Mitsuya, H.Erickson, J.W.

(1995) Structure 3: 581-590

  • DOI: 10.1016/s0969-2126(01)00192-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 protease (HIV PR), an aspartic protease, cleaves Phe-Pro bonds in the Gag and Gag-Pol viral polyproteins. Substrate-based peptide mimics constitute a major class of inhibitors of HIV PR presently being developed for AIDS treatment. One such com ...

    HIV-1 protease (HIV PR), an aspartic protease, cleaves Phe-Pro bonds in the Gag and Gag-Pol viral polyproteins. Substrate-based peptide mimics constitute a major class of inhibitors of HIV PR presently being developed for AIDS treatment. One such compound, KNI-272, which incorporates allophenylnorstatine (Apns)-thioproline (Thp) in place of Phe-Pro, has potent antiviral activity and is undergoing clinical trials. The structure of the enzyme-inhibitor complex should lead to an understanding of the structural basis for its tight binding properties and provide a framework for interpreting the emerging resistance to this drug.

    Related Citations: 
    • Crystal Structure of a Tethered Dimer of HIV-1 Proteinase Complexed with an Inhibitor
      Bhat, T.N., Baldwin, E.T., Liu, B., Cheng, Y.-S.E., Erickson, J.W.
      (1994) Nat Struct Biol 1: 552
    • Structure-Based Inhibitors of HIV-1 Protease
      Wlodawer, A., Erickson, J.W.
      (1993) Annu Rev Biochem 62: 543

    Organizational Affiliation

    Frederick Biomedical Supercomputing Center, SAIC-Frederick, NCI-Frederick Cancer Research and Development Center, Maryland 21702, USA.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEAB99Human immunodeficiency virus 1Mutation(s): 0 
EC: (UniProt), (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 KNI

Download CCD File 
C33 H41 N5 O6 S2
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KNIΔH:  0   kJ/mol  BindingDB
KNIΔG:  53.91999816894531   kJ/mol  BindingDB
KNIΔG:  48.4900016784668   kJ/mol  BindingDB
KNIΔG:  45.560001373291016   kJ/mol  BindingDB
KNI-TΔS:  33.040000915527344   kJ/mol  BindingDB
KNI-TΔS:  43.08000183105469   kJ/mol  BindingDB
KNIΔG:  48.4900016784668   kJ/mol  BindingDB
KNIΔH:  20.059999465942383   kJ/mol  BindingDB
KNIΔG:  55.59000015258789   kJ/mol  BindingDB
KNIΔH:  40.130001068115234   kJ/mol  BindingDB
KNI-TΔS:  65.23999786376953   kJ/mol  BindingDB
KNIΔG:  51.83000183105469   kJ/mol  BindingDB
KNIΔG:  50.58000183105469   kJ/mol  BindingDB
KNIΔG:  53.5   kJ/mol  BindingDB
KNIΔH:  12.960000038146973   kJ/mol  BindingDB
KNIΔH:  25.079999923706055   kJ/mol  BindingDB
KNI-TΔS:  59.38999938964844   kJ/mol  BindingDB
KNIKi:  0.3700000047683716   nM  BindingDB
KNIΔG:  41.79999923706055   kJ/mol  BindingDB
KNIΔH:  2.0899999141693115   kJ/mol  BindingDB
KNI-TΔS:  79.04000091552734   kJ/mol  BindingDB
KNI-TΔS:  70.66000366210938   kJ/mol  BindingDB
KNIΔH:  31.350000381469727   kJ/mol  BindingDB
KNIKi:  0.7400000095367432   nM  BindingDB
KNIKi:  0.6000000238418579   nM  BindingDB
KNI-TΔS:  64.81999969482422   kJ/mol  BindingDB
KNIKi:  1.100000023841858   nM  BindingDB
KNIΔH:  0.07999999821186066   kJ/mol  BindingDB
KNIKi:  0.005500000435858965   nM  Binding MOAD
KNIΔG:  56.43000030517578   kJ/mol  BindingDB
KNI-TΔS:  80.29000091552734   kJ/mol  BindingDB
KNI-TΔS:  30.950000762939453   kJ/mol  BindingDB
KNIΔG:  52.25   kJ/mol  BindingDB
KNI-TΔS:  45.59000015258789   kJ/mol  BindingDB
KNI-TΔS:  32.20000076293945   kJ/mol  BindingDB
KNIΔG:  54.34000015258789   kJ/mol  BindingDB
KNI-TΔS:  76.54000091552734   kJ/mol  BindingDB
KNIΔH:  8.359999656677246   kJ/mol  BindingDB
KNIΔH:  14.210000038146973   kJ/mol  BindingDB
KNIKi:  1.7000000476837158   nM  BindingDB
KNIΔG:  45.97999954223633   kJ/mol  BindingDB
KNIΔH:  8.779999732971191   kJ/mol  BindingDB
KNIΔH:  12.119999885559082   kJ/mol  BindingDB
KNIΔH:  9.609999656677246   kJ/mol  BindingDB
KNI-TΔS:  43.91999816894531   kJ/mol  BindingDB
KNIΔH:  12.539999961853027   kJ/mol  BindingDB
KNIΔH:  22.56999969482422   kJ/mol  BindingDB
KNIΔH:  12.119999885559082   kJ/mol  BindingDB
KNIΔG:  62.279998779296875   kJ/mol  BindingDB
KNI-TΔS:  66.48999786376953   kJ/mol  BindingDB
KNIΔH:  30.510000228881836   kJ/mol  BindingDB
KNI-TΔS:  64.81999969482422   kJ/mol  BindingDB
KNIKi:  0.5799999833106995   nM  BindingDB
KNI-TΔS:  34.290000915527344   kJ/mol  BindingDB
KNIΔG:  50.15999984741211   kJ/mol  BindingDB
KNI-TΔS:  60.63999938964844   kJ/mol  BindingDB
KNIΔG:  40.130001068115234   kJ/mol  BindingDB
KNIΔH:  21.739999771118164   kJ/mol  BindingDB
KNI-TΔS:  42.25   kJ/mol  BindingDB
KNIKi:  0.009999999776482582   nM  BindingDB
KNIKi:  0.8999999761581421   nM  BindingDB
KNIΔG:  52.66999816894531   kJ/mol  BindingDB
KNI-TΔS:  46.41999816894531   kJ/mol  BindingDB
KNI-TΔS:  75.27999877929688   kJ/mol  BindingDB
KNIΔG:  56.0099983215332   kJ/mol  BindingDB
KNIΔG:  38.040000915527344   kJ/mol  BindingDB
KNIKi :  0.005500000435858965   nM  PDBBind
KNIKi:  1.7000000476837158   nM  BindingDB
KNIΔH:  10.869999885559082   kJ/mol  BindingDB
KNI-TΔS:  50.27000045776367   kJ/mol  BindingDB
KNIΔH:  12.960000038146973   kJ/mol  BindingDB
KNIΔG:  51.83000183105469   kJ/mol  BindingDB
KNIΔH:  27.170000076293945   kJ/mol  BindingDB
KNI-TΔS:  46.84000015258789   kJ/mol  BindingDB
KNIΔH:  13.380000114440918   kJ/mol  BindingDB
KNIKi:  0.3799999952316284   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000562 (KNI)
Query on PRD_000562
Bkynostatin 272Peptide-like /  Enzyme inhibitor


Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 59.1β = 90
c = 62.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
MSIdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    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