4J02 | pdb_00004j02

Crystal structure of hcv ns5b polymerase in complex with [(1R)-5,8-DICHLORO-1-PROPYL-1,3,4,9-TETRAHYDROPYRANO[3,4-B]INDOL-1-YL]ACETIC ACID

• PDB DOI: https://doi.org/10.2210/pdb4J02/pdb

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


• Deposited: 2013-01-30 Released: 2013-04-17 
• Deposition Author(s): Coulombe, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 

Literature

Discovery of a novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors.

Stammers, T.A., Coulombe, R., Rancourt, J., Thavonekham, B., Fazal, G., Goulet, S., Jakalian, A., Wernic, D., Tsantrizos, Y., Poupart, M.A., Bos, M., McKercher, G., Thauvette, L., Kukolj, G., Beaulieu, P.L.

(2013) Bioorg Med Chem Lett 23: 2585-2589

• PubMed: 23545108 
• DOI: https://doi.org/10.1016/j.bmcl.2013.02.110
• Primary Citation Related Structures: 
  4IZ0, 4J02, 4J04, 4J06, 4J08, 4J0A


• PubMed Abstract: 
  

  A novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors were derived from a fragment-based approach using information from X-ray crystallographic analysis of NS5B-inhibitor complexes and iterative rounds of parallel synthesis. Structure-based drug design strategies led to the discovery of potent sub-micromolar inhibitors 11a-c and 12a-c from a weak-binding fragment-like structure 1 as a starting point.

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Organizational Affiliation: 
• Department of Chemistry, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 rue Cunard, Laval, Québec, Canada H7S 2G5. [e-mail]

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: 129.49 kDa 
• Atom Count: 9,514 
• Modeled Residue Count: 1,117 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1JE	C [auth A], F [auth B]	[(1R)-5,8-dichloro-1-propyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl]acetic acid C16 H17 Cl2 N O3 DKHFCUNJXIAWGU-MRXNPFEDSA-N
SO4	D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	E [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.76	α = 90
b = 108.34	β = 90
c = 133.06	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Coulombe, R.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary