3KNX | pdb_00003knx

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 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.180 (DCC) 

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3KNX

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 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

Macromolecule Content 

  • Total Structure Weight: 48.19 kDa 
  • Atom Count: 2,946 
  • Modeled Residue Count: 370 
  • Deposited Residue Count: 446 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
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