2F9U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel Inhibitors of Hepatitis C NS3-NS4A Serine Protease Derived from 2-Aza-bicyclo[2.2.1]heptane-3-carboxylic acid.

Venkatraman, S.Njoroge, F.G.Wu, W.Girijavallabhan, V.Prongay, A.J.Butkiewicz, N.Pichardo, J.

(2006) Bioorg Med Chem Lett 16: 1628-1632

  • DOI: 10.1016/j.bmcl.2005.12.046
  • Primary Citation of Related Structures:  
    2F9U

  • PubMed Abstract: 
  • Prolonged hepatitis C infection is the leading cause for cirrhosis of the liver and hepatocellular carcinoma. The etiological agent HCV virus codes a single polyprotein of approximately 3000 amino acids that is processed with the help of a serine protease NS3A to produce structural and non-structural proteins required for viral replication ...

    Prolonged hepatitis C infection is the leading cause for cirrhosis of the liver and hepatocellular carcinoma. The etiological agent HCV virus codes a single polyprotein of approximately 3000 amino acids that is processed with the help of a serine protease NS3A to produce structural and non-structural proteins required for viral replication. Inhibition of NS3 protease can potentially be used to develop drugs for treatment of HCV infections. Herein, we report the development of a series of novel NS3 serine protease inhibitors derived from 2-aza-bicyclo[2.2.1]-heptane carboxylic acid with potential therapeutic use for treatment of HCV infections.


    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, K-15, MS-3545, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Srikanth.Venkatraman@spcorp.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 protease/helicase'A, C199Hepacivirus CMutation(s): 0 
Gene Names: NS3 protease domain ( residues 1027-1207 of the polyprotein).
UniProt
Find proteins for Q91RS4 (Hepacivirus C)
Explore Q91RS4 
Go to UniProtKB:  Q91RS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91RS4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
polyproteinB, D23N/AMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5NH
Query on 5NH

Download Ideal Coordinates CCD File 
F [auth A]1,1-DIMETHYLETHYL [1-CYCLOHEXYL-2-[3-[[[1-[2-[[2-[[2-(DIMETHYLAMINO)-2-OXO-1-PHENYLETHYL]AMINO]-2-OXOETHYL]AMINO]-1,2-DIOXOETHYL]PENTYL]AMINO]CARBONYL]-2-AZABICYCLO[2.2.1]HEPTAN-2-YL]-2-OXOETHYL]CARBAMATE
C39 H58 N6 O8
YGRWTFVDMXHDOB-KTARVVEZSA-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
5NH PDBBind:  2F9U Ki: 41 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.04α = 90
b = 225.04β = 90
c = 75.44γ = 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: 2006-06-06
    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