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


Ligand Structure Quality Assessment 


This is version 1.3 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
  • Primary Citation of Related Structures:  
    2A4R

  • 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.


    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 protease/helicaseA, C200Hepacivirus CMutation(s): 0 
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
Ns4a peptideB, 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
BNH (Subject of Investigation/LOI)
Query on BNH

Download Ideal Coordinates CCD File 
F [auth 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 Ideal Coordinates CCD File 
E [auth A], G [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BNH PDBBind:  2A4R Ki: 15 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations