2A4G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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
  • Primary Citation of Related Structures:  
    2A4G

  • 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 the protease revealed the importance of the P'2 moiety ...

    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: 
    • 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
    • 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 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:  (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 P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Protein Feature View
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  • 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 Q9QP61 (Hepatitis C virus subtype 1b)
Explore Q9QP61 
Go to UniProtKB:  Q9QP61
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNH (Subject of Investigation/LOI)
Query on UNH

Download Ideal Coordinates CCD File 
F [auth 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
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
UNH PDBBind:  2A4G Ki: 66 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 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
b = 224.392β = 90
c = 75.334γ = 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



Ligand Structure Quality Assessment  



Entry History 

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: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations