2F9U

HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with a P2 norborane

• PDB DOI: https://doi.org/10.2210/pdb2F9U/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-12-06 Released: 2006-06-06 
• Deposition Author(s): Venkatraman, S., Njoroge, F.G., Wu, W., Girijavallabhan, V., Prongay, A.J., Butkiewicz, N., Pichardo, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.286 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Novel Inhibitors of Hepatitis C NS3-NS4A Serine Protease Derived from 2-Aza-bicyclo[2.2.1]heptane-3-carboxylic acid.

Venkatraman, S., Njoroge, F.G., Wu, W., Girijavallabhan, V., Prongay, A.J., Butkiewicz, N., Pichardo, J.

(2006) Bioorg Med Chem Lett 16: 1628-1632

• PubMed: 16413182 
• DOI: https://doi.org/10.1016/j.bmcl.2005.12.046
• Primary Citation of Related Structures:  
  2F9U


• PubMed Abstract: 
  

  Prolonged hepatitis C infection is the leading cause for cirrhosis of the liver and hepatocellular carcinoma. The etiological agent HCV virus codes a single polyprotein of approximately 3000 amino acids that is processed with the help of a serine protease NS3A to produce structural and non-structural proteins required for viral replication. Inhibition of NS3 protease can potentially be used to develop drugs for treatment of HCV infections. Herein, we report the development of a series of novel NS3 serine protease inhibitors derived from 2-aza-bicyclo[2.2.1]-heptane carboxylic acid with potential therapeutic use for treatment of HCV infections.

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Organizational Affiliation: 

Schering Plough Research Institute, K-15, MS-3545, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 47.86 kDa 
• Atom Count: 2,945 
• Modelled Residue Count: 377 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease/helicase'	A, C	199	Hepacivirus hominis	Mutation(s): 0  Gene Names: NS3 protease domain ( residues 1027-1207 of the polyprotein).
UniProt
Find proteins for Q91RS4 (Hepacivirus hominis) Explore Q91RS4  Go to UniProtKB:  Q91RS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
polyprotein	B, D	23	N/A	Mutation(s): 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NH	F [auth A]	1,1-DIMETHYLETHYL [1-CYCLOHEXYL-2-[3-[[[1-[2-[[2-[[2-(DIMETHYLAMINO)-2-OXO-1-PHENYLETHYL]AMINO]-2-OXOETHYL]AMINO]-1,2-DIOXOETHYL]PENTYL]AMINO]CARBONYL]-2-AZABICYCLO[2.2.1]HEPTAN-2-YL]-2-OXOETHYL]CARBAMATE C39 H58 N6 O8 YGRWTFVDMXHDOB-KTARVVEZSA-N
ZN	E [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.286 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.04	α = 90
b = 225.04	β = 90
c = 75.44	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-06 
Deposition Author(s): Venkatraman, S., Njoroge, F.G., Wu, W., Girijavallabhan, V., Prongay, A.J., Butkiewicz, N., Pichardo, J.

Revision History  

• Version 1.0: 2006-06-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-03-13
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.5: 2024-11-20
  Changes: Structure summary