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 

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


  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03369
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
JE2
Query on JE2

Download SDF File 
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
JE-2147, AG1776, KNI-764
C32 H37 N3 O5 S
CUFQBQOBLVLKRF-RZDMPUFOSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000566 (JE2)
Query on PRD_000566
AKNI-764Peptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.203α = 90.00
b = 58.409β = 90.00
c = 62.858γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2018-01-24
    Type: Database references