2A4R

HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hepatitis C Virus NS3-4A serine protease inhibitors: Use of a P2-P1 cyclopropyl alanine combination for improved potency.

Bogen, S.Saksena, A.K.Arasappan, A.Gu, H.Njoroge, F.G.Girijavallabhan, V.Pichardo, J.Butkiewicz, N.Prongay, A.Madison, V.

(2005) Bioorg Med Chem Lett 15: 4515-4519

  • DOI: 10.1016/j.bmcl.2005.07.009
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Modification of the P(2) and P(1) side chains of earlier P(3)-capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 resulted in the discovery of compound 24 with about 10-fold improvement in potency.

    Modification of the P(2) and P(1) side chains of earlier P(3)-capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 resulted in the discovery of compound 24 with about 10-fold improvement in potency.


    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. SAR of P2' moiety with improved potency.
      Arasappan, A., Njoroge, F.G., Chan, T.Y., Bennett, F., Bogen, S.L., Chen, K., Gu, H., Hong, L., Jao, E., Liu, Y.T., Lovey, R.G., Parekh, T., Pike, R.E., Pinto, P., Santhanam, B., Venkatraman, S., Vaccaro, H., Wang, H., Yang, X., Zhu, Z., Mckittrick, B., Saksena, A.K., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Ingram, R., Malcolm, B., Prongay, A.J., Yao, N., Marten, B., Madison, V., Kemp, S., Levy, O., Lim-Wilby, M., Tamura, S., Ganguly, A.K.
      (2005) Bioorg Med Chem Lett 15: 4180
    • The Crystal Structure of Hepatitis C Virus NS3 proteinase Reveals a Trypsin-like fold and a Structural Zinc Binding Site.
      Love, R.A., Parge, H.E., Wickersham, J.A., Hostomsky, Z., Habuka, N., Moomaw, E.W., Adachi, T., Hostomska, Z.
      (1996) Cell 87: 331
    • Complex of NS3 protease and NS4a peptide of BK strain hepatitis C virus: A 2.2A resolution structure in a hexagonal crystal form.
      Yan, Y., Li, Y., Munshi, S., Sardana, V., Cole, J.L., Sardana, M., Steinkuehler, C., Tomei, L., De Francesco, R., Kuo, L.C., Chen, Z.
      (1998) Protein Sci 7: 837
    • Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two protease-inhibitor complexes.
      DiMarco, S., Rizzi, M., Volpari, C., Walsh, M.A., Narjes, F., Colarusso, S., De Francesco, R., Matassa, V.G., Sollazzo, M.
      (2000) J Biol Chem 275: 7152

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ns4a peptide
B, D
23N/AMutation(s): 1 
Find proteins for O39914 (Hepacivirus C)
Go to UniProtKB:  O39914

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 protease/helicase
A, C
200Hepacivirus CMutation(s): 0 
Find proteins for Q91RS4 (Hepacivirus C)
Go to UniProtKB:  Q91RS4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNH
Query on BNH

Download CCD File 
A
[(N-{3-[(N-{CYCLOHEXYL[(ISOBUTOXYCARBONYL)AMINO]ACETYL}-3-CYCLOPROPYLALANYL)AMINO]-4-CYCLOPROPYL-2-OXOBUTANOYL}GLYCYL)AMINO](PHENYL)ACETIC ACID
C36 H51 N5 O9
VZZMJPCOMQVXJP-ZHTHUIBPSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BNHKi:  15   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.201 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.603α = 90
b = 223.603β = 90
c = 75.354γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance