2I4V

HIV-1 protease I84V, L90M with TMC126


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    2I4D, 2I4U, 2I4V, 2I4W, 2I4X

  • 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 is a major factor limiting their broader clinical use ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: gag
EC: 3.4.23.16
UniProt
Find proteins for Q903J0 (Human immunodeficiency virus 1)
Explore Q903J0 
Go to UniProtKB:  Q903J0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DJR (Subject of Investigation/LOI)
Query on DJR

Download Ideal Coordinates CCD File 
C [auth B](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
Binding Affinity Annotations 
IDSourceBinding Affinity
DJR BindingDB:  2I4V Ki: min: 0.01, max: 14 (nM) from 5 assay(s)
EC50: 1.2 (nM) from 1 assay(s)
Binding MOAD:  2I4V Ki: 6.30e-3 (nM) from 1 assay(s)
PDBBind:  2I4V Ki: 6.30e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.33α = 90
b = 86.284β = 90
c = 45.958γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
X-PLORrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations