2P59

Crystal Structure of Hepatitis C Virus NS3.4A protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2P59

  • 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 bond donors on the P4 capping group of tetrapeptide-based inhibitors result in increased binding potency to the NS3 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3A, B181Hepacivirus CMutation(s): 0 
Gene Names: NS3 protease domain
UniProt
Find proteins for Q91RS4 (Hepacivirus C)
Explore Q91RS4 
Go to UniProtKB:  Q91RS4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptideC, D21N/AMutation(s): 0 
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GG4 (Subject of Investigation/LOI)
Query on GG4

Download Ideal Coordinates CCD File 
E [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
GG4 PDBBind:  2P59 Ki: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.87α = 90
b = 225.87β = 90
c = 75.71γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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