2A4G

Hepatitis C Protease NS3-4A serine protease with Ketoamide Inhibitor SCH225724 Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 4180-4184

  • DOI: 10.1016/j.bmcl.2005.06.091
  • Also Cited By: 2OC1, 2OC8, 2OC7, 2OC0, 2OBQ, 2OBO, 2GVF, 2A4R, 2A4Q

  • PubMed Abstract: 
  • We have discovered that introduction of appropriate amino acid derivatives at P'2 position improved the binding potency of P3-capped alpha-ketoamide inhibitors of HCV NS3 serine protease. X-ray crystal structure of one of the inhibitors (43) bound to ...

    We have discovered that introduction of appropriate amino acid derivatives at P'2 position improved the binding potency of P3-capped alpha-ketoamide inhibitors of HCV NS3 serine protease. X-ray crystal structure of one of the inhibitors (43) bound to the protease revealed the importance of the P'2 moiety.


    Related Citations: 
    • 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, L.J.,Sardana, M.,Steinkuehler, C.,Tomei, L.,De Francesco, R.,Kuo, L.C.,Chen, Z.
      (1998) Protein Sci. 7: 837
    • 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
    • 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

    Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. ashok.arasappan@spcorp.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 protease/helicase
A, C
200Hepatitis C virus genotype 1a (isolate 1)Mutation(s): 0 
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Go to UniProtKB:  P26664
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS4a peptide
B, D
23Hepatitis C virus subtype 1bMutation(s): 1 
Find proteins for Q9QP61 (Hepatitis C virus subtype 1b)
Go to UniProtKB:  Q9QP61
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNH
Query on UNH

Download SDF File 
Download CCD File 
A
({1-[1-CARBAMOYL-PHENYL-METHYL)-CARBAMOYL]-METHYL}-AMINOOXALYL)-BUTYLCARBAMOYL)-3-METHYL-BUTYLCARBAMOYL)-CYCLOHEXYL-METHYL)-CARBAMIC ACID ISOBUTYL ESTER
C35 H54 N6 O8
CSOCTFLGSKTNFD-DZXSPZCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UNHKi: 66 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.193 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 224.392α = 90.00
b = 224.392β = 90.00
c = 75.334γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
X-PLORphasing
X-PLORmodel building
HKL-2000data collection
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Structure summary