3KN2

HCV NS3 Protease Domain with ketoamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

P4 capped amides and lactams as HCV NS3 protease inhibitors with improved potency and DMPK profile.

Nair, L.G.Sannigrahi, M.Bogen, S.Pinto, P.Chen, K.X.Prongay, A.Tong, X.Cheng, K.C.Girijavallabhan, V.George Njoroge, F.

(2010) Bioorg Med Chem Lett 20: 567-570

  • DOI: 10.1016/j.bmcl.2009.11.094
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • SAR studies on the extension of P3 unit of Boceprevir (1, SCH 503034) with amides and lactams and their synthesis is described. Extensive SAR studies resulted in the identification of 36 bearing 4, 4-dimethyl lactam as the new P4 cap unit with improv ...

    SAR studies on the extension of P3 unit of Boceprevir (1, SCH 503034) with amides and lactams and their synthesis is described. Extensive SAR studies resulted in the identification of 36 bearing 4, 4-dimethyl lactam as the new P4 cap unit with improved potency (K(i)( *)=15nM, EC 90=70nM) and pharmacokinetic properties (Rat AUC (PO)=3.52microMh) compared to 1.


    Organizational Affiliation

    Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. latha.nair@spcorp.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HCV NS3 Protease Domain
A, C
200Hepatitis C virus subtype 1aMutation(s): 1 
Gene Names: NS3
Find proteins for Q9ELS8 (Hepatitis C virus subtype 1a)
Go to UniProtKB:  Q9ELS8

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide KK-NS4A-KK
B, D
23N/AMutation(s): 4 
Find proteins for Q9QP61 (Hepatitis C virus subtype 1b)
Go to UniProtKB:  Q9QP61
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M66
Query on M66

Download CCD File 
A
(1R,2S,5S)-3-{(2S)-2-(2,3-dihydro-1H-inden-2-yl)-2-[({(1S)-2,2-dimethyl-1-[(2-oxopiperidin-1-yl)methyl]propyl}carbamoyl)amino]acetyl}-6,6-dimethyl-N-{(1S)-1-[oxo(prop-2-en-1-ylamino)acetyl]butyl}-3-azabicyclo[3.1.0]hexane-2-carboxamide
C40 H58 N6 O6
CRMSMBCBPAEBQR-MUIHSLIFSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.486α = 90
b = 224.486β = 90
c = 75.465γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance