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


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

  • 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 Waa ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HCV NS3 Protease
A, C
200Hepatitis C virus subtype 1aMutation(s): 0 
Find proteins for Q9ELS8 (Hepatitis C virus subtype 1a)
Go to UniProtKB:  Q9ELS8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HCV NS4a(21-39) peptide
B, D
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MCX
Query on MCX

Download SDF File 
Download CCD File 
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)carbamoyl]-L-valyl}-3-azabicyclo[3.1.0]hexane-2-carboxamide
Boceprevir derivative, bound form
C30 H51 N5 O5
WDNKLUIQDGESNW-CSCWZEDUSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MCXKi: 8 nM PDBBIND
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 = 224.020α = 90.00
b = 224.020β = 90.00
c = 75.240γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-09-19
    Type: Non-polymer description
  • Version 1.3: 2012-12-12
    Type: Other