1W5Y

HIV-1 protease in complex with fluoro substituted diol-based C2- symmetric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Symmetric Fluoro-Substituted Diol-Based HIV Protease Inhibitors. Ortho-Fluorinated and Meta-Fluorinated P1/P1'-Benzyloxy Side Groups Significantly Improve the Antiviral Activity and Preserve Binding Efficacy

Lindberg, J.Pyring, D.Loewgren, S.Rosenquist, A.Zuccarello, G.Kvarnstroem, I.Zhang, H.Vrang, L.Claesson, B.Hallberg, A.Samuelsson, B.Unge, T.

(2004) Eur.J.Biochem. 271: 4594

  • DOI: 10.1111/j.1432-1033.2004.04431.x
  • Primary Citation of Related Structures:  
  • Also Cited By: 1EBY

  • PubMed Abstract: 
  • HIV-1 protease is a pivotal enzyme in the later stages of the viral life cycle which is responsible for the processing and maturation of the virus particle into an infectious virion. As such, HIV-1 protease has become an important target for the trea ...

    HIV-1 protease is a pivotal enzyme in the later stages of the viral life cycle which is responsible for the processing and maturation of the virus particle into an infectious virion. As such, HIV-1 protease has become an important target for the treatment of AIDS, and efficient drugs have been developed. However, negative side effects and fast emerging resistance to the current drugs have necessitated the development of novel chemical entities in order to exploit different pharmacokinetic properties as well as new interaction patterns. We have used X-ray crystallography to decipher the structure-activity relationship of fluoro-substitution as a strategy to improve the antiviral activity and the protease inhibition of C2-symmetric diol-based inhibitors. In total we present six protease-inhibitor complexes at 1.8-2.3 A resolution, which have been structurally characterized with respect to their antiviral and inhibitory activities, in order to evaluate the effects of different fluoro-substitutions. These C2-symmetric inhibitors comprise mono- and difluoro-substituted benzyloxy side groups in P1/P1' and indanoleamine side groups in P2/P2'. The ortho- and meta-fluorinated P1/P1'-benzyloxy side groups proved to have the most cytopathogenic effects compared with the nonsubstituted analog and related C2-symmetric diol-based inhibitors. The different fluoro-substitutions are well accommodated in the protease S1/S1' subsites, as observed by an increase in favorable Van der Waals contacts and surface area buried by the inhibitors. These data will be used in the development of potent inhibitors with different pharmacokinetic profiles towards resistant protease mutants.


    Organizational Affiliation

    Department of Cell and Molecular Biology, BMC, Uppsala University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POL POLYPROTEIN
A, B
110Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BE6
Query on BE6

Download SDF File 
Download CCD File 
A
(2R,3R,4R,5R)-2,5-BIS[(2,5-DIFLUOROBENZYL)OXY]-3,4-DIHYDROXY-N,N'-BIS[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]HEXANEDIAMIDE
HIV-1 INHIBITOR
C38 H36 F4 N2 O8
MHRYDJWKKUNWJY-JQFCFGFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BE6Ki: 3.3 nM BINDINGMOAD
BE6Ki: 3.3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.158α = 90.00
b = 86.954β = 90.00
c = 47.218γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection