2A4Q

HCV NS3 protease with NS4a peptide and a covalently bound macrocyclic ketoamide compound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and Biological Activity of Macrocyclic Inhibitors of Hepatitis C Virus (HCV) NS3 Protease

Chen, K.X.Njoroge, F.G.Prongay, A.Pichardo, J.Madison, V.Girijavallabhan, V.

(2005) Bioorg.Med.Chem.Lett. 15: 4475-4478

  • DOI: 10.1016/j.bmcl.2005.07.033
  • Also Cited By: 2OC1, 2OC8, 2OC7, 2OC0, 2OBQ, 2OBO

  • PubMed Abstract: 
  • The 17-membered phenylalanine-based macrocycle 6 was prepared starting from 3-iodo-phenylalanine. Macrocyclization of alkene phenyl iodide 5 was effected through a palladium-catalyzed Heck reaction. The macrocyclic alpha-ketoamides were active inhibi ...

    The 17-membered phenylalanine-based macrocycle 6 was prepared starting from 3-iodo-phenylalanine. Macrocyclization of alkene phenyl iodide 5 was effected through a palladium-catalyzed Heck reaction. The macrocyclic alpha-ketoamides were active inhibitors of the HCV NS3 protease, with the C-terminal acids and amides being more potent than tert-butyl esters.


    Related Citations: 
    • 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
    • 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. 10: 7152
    • 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
    • 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


    Organizational Affiliation

    Schering-Plough Research Institute, 2015 Galloping Hill Road, K-15-3-3545, Kenilworth, NJ 07033, USA. kevin.chen@spcorp.com




Macromolecules

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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS4a peptide
B, D
23Hepacivirus CMutation(s): 1 
Gene Names: NS4a/b
Find proteins for O39914 (Hepacivirus C)
Go to UniProtKB:  O39914
Small Molecules
Ligands 3 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
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
FNH
Query on FNH

Download SDF File 
Download CCD File 
A
(2R)-({N-[(3S)-3-({[(3S,6S)-6-CYCLOHEXYL-5,8-DIOXO-4,7-DIAZABICYCLO[14.3.1]ICOSA-1(20),16,18-TRIEN-3-YL]CARBONYL}AMINO)-2-OXOHEXANOYL]GLYCYL}AMINO)(PHENYL)ACETIC ACID
C41 H55 N5 O8
MRGBFMHIJSOQIX-IMJQVECRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FNHKi: 66 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.191 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 224.923α = 90.00
b = 224.923β = 90.00
c = 75.317γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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