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 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HCV NS3 ProteaseA, C200Hepatitis C virus subtype 1aMutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q9ELS8 (Hepatitis C virus subtype 1a)
Explore Q9ELS8 
Go to UniProtKB:  Q9ELS8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HCV NS4a(21-39) peptideB, D23N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MCX (Subject of Investigation/LOI)
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
 Ligand Interaction
BME
Query on BME

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

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

  • Deposited Date: 2010-02-04 
  • Released Date: 2011-02-23 
  • Deposition Author(s): Prongay, A.J.

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