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 1.3 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: 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 ...

    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.


    Related Citations: 
    • Crystal Structure of the Hepatitis C Virus NS3 Protease Domain Complexed with a Synthetic NS4a Cofactor Peptide
      Kim, J.L., Morgenstern, K.A., Lin, C., Fox, T., Dwyer, M.D., Landro, J.A., Chambers, S.P., Markland, W., Lepre, C.A., O'Malley, E.T., Harbeson, S.L., Rice, C.M., Murcko, M.A., Caron, P.R., Thomson, J.A.
      (1996) Cell 87: 343
    • Hepatitis C virus NS3-4A serine protease inhibitors: Use of a P2-P1 cyclopropyl alanine combination to improve potency.
      Bogen, S., Saksena, A.K., Arasappan, A., Gu, N., Njoroge, F.G., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, A.
      (2005) Bioorg Med Chem Lett 15: 4515
    • Design and Synthesis of Depeptidized Macrocyclic Inhibitors of Hepatitis C NS3-4A Protease Using Structure-Based Drug Design
      Venkatraman, S., Njoroge, F.G., Girijavallabhan, V.M., Madison, V.S., Yao, N.H., Prongay, A.J., Butkiewicz, N., Pichardo, J.
      (2005) J Med Chem 48: 5088
    • Proline-Based Macrocyclic Inhibitors of the Hepatitis C Virus: Stereoselective Synthesis and Biological Activity.
      Chen, K.X., Njoroge, F.G., Vibulbhan, B., Prongay, A., Pichardo, J., Madison, V., Buevich, A., Chan, T.M.
      (2005) Angew Chem Int Ed Engl 44: 7024
    • Novel 2-oxoimidazolidine-4-carboxylic acid derivatives as Hepatitis C virus NS3-4A serine protease inhibitors: synthesis, activity and X-ray crystal structure of an enzyme inhibitor complex
      Arasappan, A., Njoroge, F.G., Parekh, T.N., Yang, X., Pichardo, J., Butkiewicz, N., Prongay, A., Yao, N., Girijavallabhan, V.
      (2004) Bioorg Med Chem Lett 14: 5751

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 protease/helicaseA, C201Hepacivirus CMutation(s): 0 
Gene Names: NS3 protease domain ( residues 1027-1207 of the polyprotein).
EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77))
Explore P27958 
Go to UniProtKB:  P27958
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
polyproteinB, D23N/AMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BN6 (Subject of Investigation/LOI)
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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], G [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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