3LOX | pdb_00003lox

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 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.202 (DCC) 

Starting Model: experimental
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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 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

Macromolecule Content 

  • Total Structure Weight: 48.03 kDa 
  • Atom Count: 2,934 
  • 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 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 

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.273 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.202 (DCC) 
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