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: https://doi.org/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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 protease/helicase
A, C
200Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NS4a peptide
B, D
23N/AMutation(s): 1 
UniProt
Find proteins for Q9QP61 (Hepatitis C virus subtype 1b)
Explore Q9QP61 
Go to UniProtKB:  Q9QP61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QP61
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UNH
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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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