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 

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Ligand Structure Quality Assessment 


This is version 1.5 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

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Ligand Structure Quality Assessment 


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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
  • Version 1.5: 2024-10-16
    Changes: Structure summary