3KNX

HCV NS3 protease domain with P1-P3 macrocyclic ketoamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and structure-activity relationship of P1-P3 ketoamide derived macrocyclic inhibitors of hepatitis C virus NS3 protease.

Venkatraman, S.Velazquez, F.Wu, W.Blackman, M.Chen, K.X.Bogen, S.Nair, L.Tong, X.Chase, R.Hart, A.Agrawal, S.Pichardo, J.Prongay, A.Cheng, K.C.Girijavallabhan, V.Piwinski, J.Shih, N.Y.Njoroge, F.G.

(2009) J Med Chem 52: 336-346

  • DOI: https://doi.org/10.1021/jm800940u
  • Primary Citation of Related Structures:  
    3KNX

  • PubMed Abstract: 

    Hepatitis C virus (HCV) infection is the major cause of chronic liver disease, leading to cirrhosis and hepatocellular carcinoma, and affects more than 200 million people worldwide. Although combination therapy of interferon-alpha and ribavirin is reasonably successful in treating majority of genotypes, its efficacy against the predominant genotype (genotype 1) is moderate at best, with only about 40% of the patients showing sustained virological response. Herein, the SAR leading to the discovery of a series of ketoamide derived P(1)-P(3) macrocyclic inhibitors that are more potent than the first generation clinical candidate, boceprevir (1, Sch 503034), is discussed. The optimization of these macrocyclic inhibitors identified a P(3) imide capped analogue 52 that was 20 times more potent than 1 and demonstrated good oral pharmacokinetics in rats. X-ray structure of 52 bound to NS3 protease and biological data are also discussed.


  • Organizational Affiliation

    Schering Plough Research Institute, K-15, MS-3545, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA. Srikanth.Venkatraman@spcorp.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HCV NS3 Protease
A, C
200Hepatitis C virus (isolate H77)Mutation(s): 1 
Gene Names: NS3
UniProt
Find proteins for Q9ELS8 (hepatitis C virus genotype 1a)
Explore Q9ELS8 
Go to UniProtKB:  Q9ELS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ELS8
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HCV NS4a peptide
B, D
23N/AMutation(s): 1 
UniProt
Find proteins for Q9ELS8 (hepatitis C virus genotype 1a)
Explore Q9ELS8 
Go to UniProtKB:  Q9ELS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ELS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JZT
Query on JZT

Download Ideal Coordinates CCD File 
F [auth A](2R)-2-{(3S,13S,16aS,17aR,17bS)-13-[({(1S)-1-[(4,4-dimethyl-2,6-dioxopiperidin-1-yl)methyl]-2,2-dimethylpropyl}carbamoyl)amino]-17,17-dimethyl-1,14-dioxooctadecahydro-2H-cyclopropa[3,4]pyrrolo[1,2-a][1,4]diazacyclohexadecin-3-yl}-2-hydroxy-N-prop-2-en-1-ylethanamide
C39 H64 N6 O7
OCBUWZICDFQHBN-MHXQYHMZSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
G [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.169 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.587α = 90
b = 223.587β = 90
c = 75.282γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description