2I4U

HIV-1 protease with TMC-126


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Suppression of HIV-1 Protease Inhibitor Resistance by Phosphonate-mediated Solvent Anchoring.

Cihlar, T.He, G.X.Liu, X.Chen, J.M.Hatada, M.Swaminathan, S.McDermott, M.J.Yang, Z.Y.Mulato, A.S.Chen, X.Leavitt, S.A.Stray, K.M.Lee, W.A.

(2006) J.Mol.Biol. 363: 635-647

  • DOI: 10.1016/j.jmb.2006.07.073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The introduction of human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) markedly improved the clinical outcome and control of HIV-1 infection. However, cross-resistance among PIs due to a wide spectrum of mutations in viral protease ...

    The introduction of human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) markedly improved the clinical outcome and control of HIV-1 infection. However, cross-resistance among PIs due to a wide spectrum of mutations in viral protease is a major factor limiting their broader clinical use. Here we report on the suppression of PI resistance using a covalent attachment of a phosphonic acid motif to a peptidomimetic inhibitor scaffold. The resulting phosphonate analogs maintain high binding affinity to HIV-1 protease, potent antiretroviral activity, and unlike the parent molecules, display no loss of potency against a panel of clinically important PI-resistant HIV-1 strains. As shown by crystallographic analysis, the phosphonate moiety is highly exposed to solvent with no discernable interactions with any of the enzyme active site or surface residues. We term this effect "solvent anchoring" and demonstrate that it is driven by a favorable change in the inhibitor binding entropy upon the interaction with mutant enzymes. This type of thermodynamic behavior, which was not found with the parent scaffold fully buried in the enzyme active site, is a result of the increased degeneracy of inhibitor binding states, allowing effective molecular adaptation to the expanded cavity volume of mutant proteases. This strategy, which is applicable to various PI scaffolds, should facilitate the design of novel PIs and potentially other antiviral therapeutics.


    Organizational Affiliation

    Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for Q7SSI0 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q7SSI0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DJR
Query on DJR

Download SDF File 
Download CCD File 
A
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]CARBAMATE
C28 H38 N2 O8 S
BINXAIIXOUQUKC-UIPNDDLNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DJRKi: 0 - 0 nM (94) BINDINGDB
DJREC50: 1.2 nM (94) BINDINGDB
DJRKi: 0.0027 nM BINDINGMOAD
DJRKi: 0.0027 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.530α = 90.00
b = 86.044β = 90.00
c = 46.234γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
d*TREKdata scaling
X-PLORrefinement
d*TREKdata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-08-22 
  • Released Date: 2007-08-28 
  • Deposition Author(s): Hatada, M.

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance