2P59

Crystal Structure of Hepatitis C Virus NS3.4A protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibitors of hepatitis C virus NS3.4A protease. Effect of P4 capping groups on inhibitory potency and pharmacokinetics.

Perni, R.B.Chandorkar, G.Cottrell, K.M.Gates, C.A.Lin, C.Lin, K.Luong, Y.P.Maxwell, J.P.Murcko, M.A.Pitlik, J.Rao, G.Schairer, W.C.Van Drie, J.Wei, Y.

(2007) Bioorg.Med.Chem.Lett. 17: 3406-3411

  • DOI: 10.1016/j.bmcl.2007.03.090

  • PubMed Abstract: 
  • Reversible tetrapeptide-based compounds have been shown to effectively inhibit the hepatitis C virus NS3.4A protease. Inhibition of viral replicon RNA production in Huh-7 cells has also been demonstrated. We show herein that the inclusion of hydrogen ...

    Reversible tetrapeptide-based compounds have been shown to effectively inhibit the hepatitis C virus NS3.4A protease. Inhibition of viral replicon RNA production in Huh-7 cells has also been demonstrated. We show herein that the inclusion of hydrogen bond donors on the P4 capping group of tetrapeptide-based inhibitors result in increased binding potency to the NS3.4A protease. The capping groups also impart significant effects on the pharmacokinetic profile of these inhibitors.


    Organizational Affiliation

    Vertex Pharmaceuticals, Inc., 130 Waverly Street, Cambridge, MA 02139, USA. rperni@sirtrispharma.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3
A, B
181Hepacivirus CMutation(s): 0 
Find proteins for Q91RS4 (Hepacivirus C)
Go to UniProtKB:  Q91RS4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide
C, D
21Hepatitis C virus genotype 1a (isolate H)Mutation(s): 0 
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H))
Go to UniProtKB:  P27958
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GG4
Query on GG4

Download SDF File 
Download CCD File 
B
(2S,3AS,7AS)-1-[(2S)-2-{[(2S)-2-CYCLOHEXYL-2-({[(2R)-4-NITRO-2H-PYRROL-2-YL]CARBONYL}AMINO)ACETYL]AMINO}-3,3-DIMETHYLBUTANOYL]-N-{(1S)-1-[(1R)-2-(CYCLOPROPYLAMINO)-1-HYDROXY-2-OXOETHYL]BUTYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE
C37 H57 N7 O8
HXPWPXJRIXYIRJ-MGNUMPGCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GG4Ki: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 225.870α = 90.00
b = 225.870β = 90.00
c = 75.710γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CrystalCleardata collection
PDB_EXTRACTdata extraction
DENZOdata reduction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-03-14 
  • Released Date: 2008-02-05 
  • Deposition Author(s): Perni, R.B., Wei, Y.

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance