4FE6

Crystal Structure of HIV-1 Protease in Complex with an enamino-oxindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Enamino-oxindole HIV protease inhibitors.

Eissenstat, M.Guerassina, T.Gulnik, S.Afonina, E.Silva, A.M.Ludtke, D.Yokoe, H.Yu, B.Erickson, J.

(2012) Bioorg Med Chem Lett 22: 5078-5083

  • DOI: 10.1016/j.bmcl.2012.05.120
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We have designed and synthesized a series of HIV protease inhibitors (PIs) with enamino-oxindole substituents optimized to interact with the S2' subsite of the HIV protease binding pocket. Several of these inhibitors have sub-nanomolar K(i) and antiv ...

    We have designed and synthesized a series of HIV protease inhibitors (PIs) with enamino-oxindole substituents optimized to interact with the S2' subsite of the HIV protease binding pocket. Several of these inhibitors have sub-nanomolar K(i) and antiviral IC(50) in the low nM range against WT HIV and against a panel of multi-drug resistant (MDR) strains.


    Organizational Affiliation

    Sequoia Pharmaceuticals, Inc., Gaithersburg, MD 10878, USA. eissenst@comcast.net



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV protease
A
99Human immunodeficiency virus type 1 (BRU ISOLATE)Mutation(s): 0 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0TQ
Query on 0TQ

Download CCD File 
A
(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-[({(3Z)-3-[1-(methylamino)ethylidene]-2-oxo-2,3-dihydro-1H-indol-5-yl}sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate
C32 H42 N4 O8 S
CJXWCYBPIXFWOP-PEXZKGFOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0TQKi:  0.30000001192092896   nM  Binding MOAD
0TQKi:  0.10000000149011612   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.654α = 90
b = 62.654β = 90
c = 82.361γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references