3KN2

HCV NS3 Protease Domain with ketoamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3KN2/pdb

• Classification: HYDROLASE
• Organism(s): hepatitis C virus genotype 1a, Hepatitis C virus genotype 1b (isolate Con1)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-11 Released: 2010-01-19 
• Deposition Author(s): Nair, L.G., Sannigrahi, M., Pinto, P., Bogen, S., Chen, K.X., Njoroge, G., Prongay, A.

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Experimental Data Snapshot

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

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

• PubMed: 20004570 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.094
• Primary Citation of 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.

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Organizational Affiliation: 

Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS3 Protease Domain	A, C	200	hepatitis C virus genotype 1a	Mutation(s): 1  Gene Names: NS3
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1)) Explore P26664  Go to UniProtKB:  P26664

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide KK-NS4A-KK	B, D	23	N/A	Mutation(s): 4
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1)) Explore Q9WMX2  Go to UniProtKB:  Q9WMX2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M66	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	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 
• R-Value Work: 0.200 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.486	α = 90
b = 224.486	β = 90
c = 75.465	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
X-PLOR	model building
X-PLOR	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Nair, L.G., Sannigrahi, M., Pinto, P., Bogen, S., Chen, K.X., Njoroge, G., Prongay, A.

Revision History  

• 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