3KN2 | pdb_00003kn2

HCV NS3 Protease Domain with ketoamide inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.264 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.199 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3KN2

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.bmcl.2009.11.094
  • Primary Citation Related Structures: 
    3KN2

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 48.1 kDa 
  • Atom Count: 2,976 
  • Modeled Residue Count: 370 
  • Deposited Residue Count: 446 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HCV NS3 Protease Domain
A, C
200hepatitis C virus genotype 1aMutation(s): 1 
Gene Names: NS3
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide KK-NS4A-KK
B, D
23N/AMutation(s): 4 
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Explore Q9WMX2 
Go to UniProtKB:  Q9WMX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WMX2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M66

Query on M66


Download:Ideal Coordinates CCD File
F [auth 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
ZN

Query on ZN


Download:Ideal Coordinates CCD File
E [auth A],
G [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.264 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.199 (DCC) 
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-11-27
    Changes: Data collection, Structure summary