2FLE

Structural analysis of asymmetric inhibitor bound to the HIV-1 Protease V82A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation.

Clemente, J.C.Robbins, A.Grana, P.Paleo, M.R.Correa, J.F.Villaverde, M.C.Sardina, F.J.Govindasamy, L.Agbandje-McKenna, M.McKenna, R.Dunn, B.M.Sussman, F.

(2008) J.Med.Chem. 51: 852-860

  • DOI: 10.1021/jm701170f

  • PubMed Abstract: 
  • In our quest for HIV-1 protease inhibitors that are not affected by the V82A resistance mutation, we have synthesized and tested a second generation set of C2-symmetric HIV-1 protease inhibitors that contain a cyclohexane group at P1 and/or P1'. The ...

    In our quest for HIV-1 protease inhibitors that are not affected by the V82A resistance mutation, we have synthesized and tested a second generation set of C2-symmetric HIV-1 protease inhibitors that contain a cyclohexane group at P1 and/or P1'. The binding affinity results indicate that these compounds have an improved response to the appearance of the V82A mutation than the parent compound. The X-ray structure of one of these compounds with the V82A HIV-1 PR variant provides the structural rationale for the better resistance profile of these compounds. Moreover, scrutiny of the X-ray structure suggests that the ring of the Cha side chain might be in a boat rather than in the chair conformation, a result supported by molecular dynamics simulations.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pol protein
A, B
99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
Find proteins for Q9J2R0 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q9J2R0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AI
Query on AI

Download SDF File 
Download CCD File 
B
(2S,2'S)-N,N'-[(2S,3S,4S,5S)-1-CYCLOHEXYL-3,4-DIHYDROXY-6-PHENYLHEXANE-2,5-DIYL]BIS[3-METHYL-2-({[METHYL(PYRIDIN-2-YLMETHYL)AMINO]CARBONYL}AMINO)BUTANAMIDE]
C44 H64 N8 O6
JQIFSYRTTKZQMY-UNHORJANSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AIKi: 14 nM (97) BINDINGDB
AIKi: 14 nM BINDINGMOAD
AIKi: 14 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.195α = 90.00
b = 62.195β = 90.00
c = 82.752γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description