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
  • Primary Citation of Related Structures:  
    2A4Q

  • 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 inhibitors of the HCV NS3 protease, with the C-terminal acids and amides being more potent than tert-butyl esters ...

    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: 
    • 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, 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NS4a peptideBD23N/AMutation(s): 1 
Find proteins for O39914 (Hepacivirus C)
Explore O39914 
Go to UniProtKB:  O39914
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 protease/helicase'AC200Hepacivirus CMutation(s): 0 
Find proteins for Q91RS4 (Hepacivirus C)
Explore Q91RS4 
Go to UniProtKB:  Q91RS4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FNH
Query on FNH

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
BME
Query on BME

Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-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 %)
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
b = 224.923β = 90
c = 75.317γ = 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



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