2F9V

HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Depeptidization efforts on P3-P2 a-ketoamide inhibitors of HCV NS3-4A serine protease: Effect on HCV replicon activity.

Bogen, S.L.Ruan, S.Liu, R.Agrawal, S.Pichardo, J.Prongay, A.Baroudy, B.Saksena, A.Girijavallabhan, V.Njoroge, F.G.

(2006) Bioorg Med Chem Lett 16: 1621-1627

  • DOI: https://doi.org/10.1016/j.bmcl.2005.12.013
  • Primary Citation of Related Structures:  
    2F9V

  • PubMed Abstract: 

    Depeptidization efforts of the P(3)-P(2) region of P(3) capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 are reported. We clearly established that N-methylation of the P(2) nitrogen and modification of the P(2)' carboxylic acid terminus were essential for activity in the replicon assay.


  • Organizational Affiliation

    Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. stephane.bogen@spcorp.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 protease/helicase
A, C
201Hepacivirus hominisMutation(s): 0 
Gene Names: NS3 protease domain ( residues 1027-1207 of the polyprotein).
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27958
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
polyprotein
B, D
23N/AMutation(s): 1 
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27958
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BN6
Query on BN6

Download Ideal Coordinates CCD File 
F [auth A](2S,8R,9S,15S)-15-CYCLOHEXYL-9,12-BIS(CYCLOPROPYLMETHYL)-8-HYDROXY-20-METHYL-4,7,11,14,17-PENTAOXO-2-PHENYL-18-OXA-3,6,10,12,13,16-HEXAAZAHENICOSAN-1-OIC ACID
C35 H52 N6 O9
PLFWZBVXDUFZCY-ZVVXMFRTSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BN6 PDBBind:  2F9V Ki: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.811α = 90
b = 222.811β = 90
c = 75.266γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-03-13
    Changes: Data collection, Source and taxonomy, Structure summary