2P59

Crystal Structure of Hepatitis C Virus NS3.4A protease

• PDB DOI: https://doi.org/10.2210/pdb2P59/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepacivirus hominis, Hepatitis C virus genotype 1a (isolate H77)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-14 Released: 2008-02-05 
• Deposition Author(s): Perni, R.B., Wei, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Literature

Inhibitors of hepatitis C virus NS3.4A protease. Effect of P4 capping groups on inhibitory potency and pharmacokinetics.

Perni, R.B., Chandorkar, G., Cottrell, K.M., Gates, C.A., Lin, C., Lin, K., Luong, Y.P., Maxwell, J.P., Murcko, M.A., Pitlik, J., Rao, G., Schairer, W.C., Van Drie, J., Wei, Y.

(2007) Bioorg Med Chem Lett 17: 3406-3411

• PubMed: 17482818 
• DOI: https://doi.org/10.1016/j.bmcl.2007.03.090
• Primary Citation of Related Structures:  
  2P59


• PubMed Abstract: 
  

  Reversible tetrapeptide-based compounds have been shown to effectively inhibit the hepatitis C virus NS3.4A protease. Inhibition of viral replicon RNA production in Huh-7 cells has also been demonstrated. We show herein that the inclusion of hydrogen bond donors on the P4 capping group of tetrapeptide-based inhibitors result in increased binding potency to the NS3.4A protease. The capping groups also impart significant effects on the pharmacokinetic profile of these inhibitors.

---

Organizational Affiliation: 

Vertex Pharmaceuticals, Inc., 130 Waverly Street, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.24 kDa 
• Atom Count: 2,740 
• Modelled Residue Count: 369 
• Deposited Residue Count: 404 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3	A, B	181	Hepacivirus hominis	Mutation(s): 0  Gene Names: NS3 protease domain
UniProt
Find proteins for Q91RS4 (Hepacivirus hominis) Explore Q91RS4  Go to UniProtKB:  Q91RS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	C, D	21	N/A	Mutation(s): 0
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GG4	E [auth B]	(2S,3AS,7AS)-1-[(2S)-2-{[(2S)-2-CYCLOHEXYL-2-({[(2R)-4-NITRO-2H-PYRROL-2-YL]CARBONYL}AMINO)ACETYL]AMINO}-3,3-DIMETHYLBUTANOYL]-N-{(1S)-1-[(1R)-2-(CYCLOPROPYLAMINO)-1-HYDROXY-2-OXOETHYL]BUTYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE C37 H57 N7 O8 HXPWPXJRIXYIRJ-MGNUMPGCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GG4	PDBBind:  2P59	Ki: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.87	α = 90
b = 225.87	β = 90
c = 75.71	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Perni, R.B., Wei, Y.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance