1KZK

JE-2147-HIV Protease Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Anisotropic Dynamics of the JE-2147-HIV Protease Complex: Drug Resistance and Thermodynamic Binding Mode Examined in a 1.09 A Structure

Reiling, K.K.Endres, N.F.Dauber, D.S.Craik, C.S.Stroud, R.M.

(2002) Biochemistry 41: 4582-4594

  • DOI: 10.1021/bi011781z
  • Primary Citation of Related Structures:  
    1KZK

  • PubMed Abstract: 
  • The structure of HIV protease (HIV Pr) bound to JE-2147 (also named AG1776 or KNI-764) is determined here to 1.09 A resolution. This highest-resolution structure for HIV Pr allows refinement of anisotropic displacement parameters (ADPs) for all atoms ...

    The structure of HIV protease (HIV Pr) bound to JE-2147 (also named AG1776 or KNI-764) is determined here to 1.09 A resolution. This highest-resolution structure for HIV Pr allows refinement of anisotropic displacement parameters (ADPs) for all atoms. Clustering based on the directional information in ADPs defines two sets of subdomains such that within each set, subdomains undergo similar anisotropic motion. These sets are (a) the core of monomer A grouped with both substrate-binding flaps and (b) the core of monomer B coupled to both catalytic aspartates (25A/B). The four-stranded beta-sheet (1-4 A/B and 95-99 A/B) that forms a significant part of the dimer interface exhibits large anisotropic amplitudes that differ from those of the other sets of subdomains. JE-2147 is shown here to be a picomolar inhibitor (K(i) = 41 +/- 18 pM). The structure is used to interpret the mechanism of association of JE-2147, a second-generation inhibitor for which binding is enthalpically driven, with respect to first-generation inhibitors for which binding is predominantly entropically driven [Velazquez-Campoy, A., et al. (2001) Arch. Biochem. Biophys. 390, 169-175]. Relative to the entropically driven inhibitor complexes, the JE-2147-HIV Pr complex exhibits an approximately 0.5 A movement of the substrate flaps in toward the substrate, suggesting a more compatible enthalpically driven association. Domains of the protease identified by clustering of ADPs also suggest a model of enthalpy-entropy compensation for all HIV Pr inhibitors in which dynamic coupling of the flaps is offset by an increased level of motion of the beta-sheet domain of the dimer interface (1-4 A/B and 95-99 A/B).


    Related Citations: 
    • Structure-Activity Relationship of Small-Sized HIV Protease Inhibitors Containing Allophenylnorstatine
      Mimoto, T., Kato, R., Takaku, H., Nojima, S., Terashima, K., Misawa, S., Fukazawa, T., Ueno, T., Sato, H., Shintani, M., Kiso, Y., Hayashi, H.
      (1999) J Med Chem 42: 1789

    Organizational Affiliation

    Department of Biochemistry and Biophysics, Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseAB99Human immunodeficiency virusMutation(s): 1 
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JE2
Query on JE2

Download CCD File 
A
(4R)-3-{(2S,3S)-2-hydroxy-3-[(3-hydroxy-2-methylbenzoyl)amino]-4-phenylbutanoyl}-5,5-dimethyl-N-(2-methylbenzyl)-1,3-thiazolidine-4-carboxamide
C32 H37 N3 O5 S
CUFQBQOBLVLKRF-RZDMPUFOSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JE2ΔH:  28.84000015258789   kJ/mol  BindingDB
JE2ΔH:  12.119999885559082   kJ/mol  BindingDB
JE2ΔH:  25.079999923706055   kJ/mol  BindingDB
JE2ΔG:  57.27000045776367   kJ/mol  BindingDB
JE2ΔH:  73.1500015258789   kJ/mol  BindingDB
JE2ΔH:  15.470000267028809   kJ/mol  BindingDB
JE2Ki:  0.3199999928474426   nM  BindingDB
JE2ΔH:  25.079999923706055   kJ/mol  BindingDB
JE2ΔG:  53.91999816894531   kJ/mol  BindingDB
JE2ΔH:  15.050000190734863   kJ/mol  BindingDB
JE2ΔG:  60.61000061035156   kJ/mol  BindingDB
JE2-TΔS:  59.810001373291016   kJ/mol  BindingDB
JE2ΔH:  33.439998626708984   kJ/mol  BindingDB
JE2-TΔS:  62.310001373291016   kJ/mol  BindingDB
JE2-TΔS:  79.04000091552734   kJ/mol  BindingDB
JE2ΔG:  62.279998779296875   kJ/mol  BindingDB
JE2ΔG:  57.68000030517578   kJ/mol  BindingDB
JE2Ki:  0.550000011920929   nM  BindingDB
JE2ΔH:  14.630000114440918   kJ/mol  BindingDB
JE2ΔH:  13.380000114440918   kJ/mol  BindingDB
JE2ΔH:  18.389999389648438   kJ/mol  BindingDB
JE2ΔH:  8.359999656677246   kJ/mol  BindingDB
JE2-TΔS:  59.38999938964844   kJ/mol  BindingDB
JE2ΔG:  51.83000183105469   kJ/mol  BindingDB
JE2ΔG:  28.84000015258789   kJ/mol  BindingDB
JE2ΔH:  14.210000038146973   kJ/mol  BindingDB
JE2Ki:  0.07999999821186066   nM  BindingDB
JE2-TΔS:  43.08000183105469   kJ/mol  BindingDB
JE2ΔH:  13.789999961853027   kJ/mol  BindingDB
JE2-TΔS:  61.47999954223633   kJ/mol  BindingDB
JE2ΔG:  52.25   kJ/mol  BindingDB
JE2ΔG:  61.45000076293945   kJ/mol  BindingDB
JE2ΔH:  21.31999969482422   kJ/mol  BindingDB
JE2ΔH:  24.239999771118164   kJ/mol  BindingDB
JE2ΔH:  16.299999237060547   kJ/mol  BindingDB
JE2-TΔS:  65.6500015258789   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2-TΔS:  60.22999954223633   kJ/mol  BindingDB
JE2-TΔS:  51.0099983215332   kJ/mol  BindingDB
JE2-TΔS:  28.030000686645508   kJ/mol  BindingDB
JE2ΔG:  62.279998779296875   kJ/mol  BindingDB
JE2-TΔS:  64.81999969482422   kJ/mol  BindingDB
JE2Ki:  9.399999618530273   nM  BindingDB
JE2ΔH:  15.470000267028809   kJ/mol  BindingDB
JE2ΔG:  44.310001373291016   kJ/mol  BindingDB
JE2Ki:  0.04100000113248825   nM  Binding MOAD
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2ΔG:  55.18000030517578   kJ/mol  BindingDB
JE2ΔH:  6.690000057220459   kJ/mol  BindingDB
JE2ΔG:  51   kJ/mol  BindingDB
JE2ΔG:  35.529998779296875   kJ/mol  BindingDB
JE2-TΔS:  65.6500015258789   kJ/mol  BindingDB
JE2-TΔS:  28.030000686645508   kJ/mol  BindingDB
JE2ΔG:  42.63999938964844   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2ΔG:  49.31999969482422   kJ/mol  BindingDB
JE2ΔG:  53.5   kJ/mol  BindingDB
JE2ΔG:  55.18000030517578   kJ/mol  BindingDB
JE2Ki:  0.10999999940395355   nM  BindingDB
JE2ΔH:  18.389999389648438   kJ/mol  BindingDB
JE2ΔH:  31.350000381469727   kJ/mol  BindingDB
JE2-TΔS:  77.37000274658203   kJ/mol  BindingDB
JE2Ki:  0.33000001311302185   nM  BindingDB
JE2ΔG:  60.189998626708984   kJ/mol  BindingDB
JE2-TΔS:  30.530000686645508   kJ/mol  BindingDB
JE2Ki:  0.1899999976158142   nM  BindingDB
JE2ΔG:  51   kJ/mol  BindingDB
JE2-TΔS:  64.81999969482422   kJ/mol  BindingDB
JE2ΔH:  5.019999980926514   kJ/mol  BindingDB
JE2ΔG:  62.279998779296875   kJ/mol  BindingDB
JE2Ki:  0.019999999552965164   nM  BindingDB
JE2ΔH:  0   kJ/mol  BindingDB
JE2ΔH:  9.199999809265137   kJ/mol  BindingDB
JE2ΔH:  15.050000190734863   kJ/mol  BindingDB
JE2ΔH:  12.119999885559082   kJ/mol  BindingDB
JE2-TΔS:  35.119998931884766   kJ/mol  BindingDB
JE2Ki :  0.04100000113248825   nM  PDBBind
JE2ΔH:  43.470001220703125   kJ/mol  BindingDB
JE2-TΔS:  57.29999923706055   kJ/mol  BindingDB
JE2-TΔS:  44.75   kJ/mol  BindingDB
JE2ΔH:  35.529998779296875   kJ/mol  BindingDB
JE2ΔG:  54.7599983215332   kJ/mol  BindingDB
JE2-TΔS:  65.23999786376953   kJ/mol  BindingDB
JE2ΔG:  53.09000015258789   kJ/mol  BindingDB
JE2ΔG:  49.7400016784668   kJ/mol  BindingDB
JE2ΔG:  48.4900016784668   kJ/mol  BindingDB
JE2ΔH:  7.940000057220459   kJ/mol  BindingDB
JE2ΔG:  49.7400016784668   kJ/mol  BindingDB
JE2-TΔS:  28.860000610351562   kJ/mol  BindingDB
JE2-TΔS:  43.91999816894531   kJ/mol  BindingDB
JE2-TΔS:  71.11000061035156   kJ/mol  BindingDB
JE2-TΔS:  102.05999755859375   kJ/mol  BindingDB
JE2Ki:  0.10999999940395355   nM  BindingDB
JE2ΔH:  27.59000015258789   kJ/mol  BindingDB
JE2ΔH:  10.869999885559082   kJ/mol  BindingDB
JE2-TΔS:  58.970001220703125   kJ/mol  BindingDB
JE2ΔH:  25.5   kJ/mol  BindingDB
JE2Ki:  0.029999999329447746   nM  BindingDB
JE2Ki:  0.03999999910593033   nM  BindingDB
JE2-TΔS:  41   kJ/mol  BindingDB
JE2ΔH:  8.779999732971191   kJ/mol  BindingDB
JE2ΔG:  59.77000045776367   kJ/mol  BindingDB
JE2ΔG:  54.34000015258789   kJ/mol  BindingDB
JE2ΔG:  50.15999984741211   kJ/mol  BindingDB
JE2ΔG:  54.34000015258789   kJ/mol  BindingDB
JE2-TΔS:  28.860000610351562   kJ/mol  BindingDB
JE2-TΔS:  30.950000762939453   kJ/mol  BindingDB
JE2ΔG:  47.22999954223633   kJ/mol  BindingDB
JE2ΔG:  45.97999954223633   kJ/mol  BindingDB
JE2ΔH:  31.770000457763672   kJ/mol  BindingDB
JE2ΔH:  30.93000030517578   kJ/mol  BindingDB
JE2-TΔS:  61.900001525878906   kJ/mol  BindingDB
JE2-TΔS:  26.360000610351562   kJ/mol  BindingDB
JE2ΔG:  38.869998931884766   kJ/mol  BindingDB
JE2ΔG:  40.54999923706055   kJ/mol  BindingDB
JE2-TΔS:  33.040000915527344   kJ/mol  BindingDB
JE2-TΔS:  34.290000915527344   kJ/mol  BindingDB
JE2ΔG:  53.09000015258789   kJ/mol  BindingDB
JE2ΔG:  41.79999923706055   kJ/mol  BindingDB
JE2-TΔS:  30.110000610351562   kJ/mol  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000566 (JE2)
Query on PRD_000566
AKNI-764Peptide-like /  Enzyme inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.203α = 90
b = 58.409β = 90
c = 62.858γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-03
    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
  • Version 1.4: 2018-01-24
    Changes: Database references