3LOX

HCV NS3-4a protease domain with a ketoamide inhibitor derivative of Boceprevir bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The introduction of P4 substituted 1-methylcyclohexyl groups into Boceprevir: a change in direction in the search for a second generation HCV NS3 protease inhibitor.

Bennett, F.Huang, Y.Hendrata, S.Lovey, R.Bogen, S.L.Pan, W.Guo, Z.Prongay, A.Chen, K.X.Arasappan, A.Venkatraman, S.Velazquez, F.Nair, L.Sannigrahi, M.Tong, X.Pichardo, J.Cheng, K.C.Girijavallabhan, V.M.Saksena, A.K.Njoroge, F.G.

(2010) Bioorg Med Chem Lett 20: 2617-2621

  • DOI: https://doi.org/10.1016/j.bmcl.2010.02.063
  • Primary Citation of Related Structures:  
    3LOX

  • PubMed Abstract: 

    In the search for a second generation HCV protease inhibitor, molecular modeling studies of the X-ray crystal structure of Boceprevir1 bound to the NS3 protein suggest that expansion into the S4 pocket could provide additional hydrophobic Van der Waals interactions. Effective replacement of the P4 tert-butyl with a cyclohexylmethyl ligand led to inhibitor 2 with improved enzyme and replicon activities. Subsequent modeling and SAR studies led to the pyridine 38 and sulfone analogues 52 and 53 with vastly improved PK parameters in monkeys, forming a new foundation for further exploration.


  • Organizational Affiliation

    Schering-Plough Research Institute, K-15-A-3545, Kenilworth, NJ 07033, USA. frank.bennett@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 genotype 1aMutation(s): 0 
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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HCV NS4a(21-39) peptide
B, D
23N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MCX
Query on MCX

Download Ideal Coordinates CCD File 
F [auth A](1R,2S,5S)-N-[(2S,3R)-4-amino-1-cyclobutyl-3-hydroxy-4-oxobutan-2-yl]-6,6-dimethyl-3-{3-methyl-N-[(1-methylcyclohexyl)c arbamoyl]-L-valyl}-3-azabicyclo[3.1.0]hexane-2-carboxamide
C30 H51 N5 O5
WDNKLUIQDGESNW-CSCWZEDUSA-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
Binding Affinity Annotations 
IDSourceBinding Affinity
MCX PDBBind:  3LOX Ki: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.02α = 90
b = 224.02β = 90
c = 75.24γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-19
    Changes: Non-polymer description
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary