4I32 | pdb_00004i32

Crystal structure of HCV NS3/4A D168V protease complexed with compound 4

• PDB DOI: https://doi.org/10.2210/pdb4I32/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Hepatitis C virus (isolate Japanese)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-11-23 Released: 2013-01-02 
• Deposition Author(s): Lemke, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Molecular Mechanism by Which a Potent Hepatitis C Virus NS3-NS4A Protease Inhibitor Overcomes Emergence of Resistance.

O'Meara, J.A., Lemke, C.T., Godbout, C., Kukolj, G., Lagace, L., Moreau, B., Thibeault, D., White, P.W., Llinas-Brunet, M.

(2013) J Biological Chem 288: 5673-5681

• PubMed: 23271737 
• DOI: https://doi.org/10.1074/jbc.M112.439455
• Primary Citation Related Structures: 
  4I31, 4I32, 4I33


• PubMed Abstract: 
  

  Although optimizing the resistance profile of an inhibitor can be challenging, it is potentially important for improving the long term effectiveness of antiviral therapy. This work describes our rational approach toward the identification of a macrocyclic acylsulfonamide that is a potent inhibitor of the NS3-NS4A proteases of all hepatitis C virus genotypes and of a panel of genotype 1-resistant variants. The enhanced potency of this compound versus variants D168V and R155K facilitated x-ray determination of the inhibitor-variant complexes. In turn, these structural studies revealed a complex molecular basis of resistance and rationalized how such compounds are able to circumvent these mechanisms.

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Organizational Affiliation: 
• Boehringer Ingelheim (Canada) Limited, Research and Development, Laval, Quebec H7S 2G5, Canada. [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)

Macromolecule Content 

• Total Structure Weight: 44.85 kDa 
• Atom Count: 3,039 
• Modeled Residue Count: 390 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	187	Hepatitis C virus (isolate Japanese)	Mutation(s): 1  Gene Names: POLG_HCVJA EC: 3.4.22 (PDB Primary Data), 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV non-structural protein 4A	C, D	17	Hepatitis C virus (isolate Japanese)	Mutation(s): 0
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BV	F [auth A], G [auth B]	(2R,6S,7E,10E,13aR,14aR,16aS)-2-{[7-methoxy-8-methyl-2-(propan-2-yloxy)quinolin-4-yl]oxy}-N-[(1-methylcyclopropyl)sulfonyl]-6-{[(1-methyl-1H-pyrazol-3-yl)carbonyl]amino}-5,16-dioxo-1,2,3,6,9,12,13,13a,14,15,16,16a-dodecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecine-14a(5H)-carboxamide C41 H51 N7 O9 S ZHIQOLBHZJFLCW-QVARATBXSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.671	α = 90
b = 93.671	β = 90
c = 81.83	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-02 
Deposition Author(s): Lemke, C.T.

Revision History  

• Version 1.0: 2013-01-02
  Type: Initial release
  
• Version 1.1: 2013-01-09
  Changes: Database references
• Version 1.2: 2013-03-13
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary