4GMC | pdb_00004gmc

Crystal structure of HCV NS5B polymerase in complex with a thumb inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GMC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Hepatitis C virus isolate HC-J4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-15 Released: 2013-02-20 
• Deposition Author(s): Coulombe, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.218 (DCC) 

Starting Model: experimental

Literature

Allosteric N-acetamide-indole-6-carboxylic acid thumb pocket 1 inhibitors of hepatitis C virus NS5B polymerase - Acylsulfonamides and acylsulfamides as carboxylic acid replacements

Beaulieu, P.L., Coulombe, R., Gillard, J., Brochu, C., Duan, J., Garneau, M., Jolicoeur, E., Kuhn, P., Poupart, M.A., Rancourt, J., Stammers, T.A., Thavonekham, B., Kukolj, G.

(2013) Can J Chem 91: 66-81

• DOI: https://doi.org/10.1139/cjc-2012-0319

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 129.53 kDa 
• Atom Count: 8,692 
• Modeled Residue Count: 1,100 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5B polymerase	A, B	576	Hepatitis C virus isolate HC-J4	Mutation(s): 0  Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4)) Explore O92972  Go to UniProtKB:  O92972

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BI	E [auth B]	3-cyclohexyl-2-(furan-3-yl)-1-[2-(morpholin-4-yl)-2-oxoethyl]-N-(phenylsulfonyl)-1H-indole-6-carboxamide C31 H33 N3 O6 S GQYVRIAVVLRHPU-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.257 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.218 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.24	α = 90
b = 106.26	β = 90
c = 133.33	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Coulombe, R.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description