5TWM

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb5TWM/pdb

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Hepatitis C virus JFH-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-11-14 Released: 2017-03-15 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.207 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

The discovery of a pan-genotypic, primer grip inhibitor of HCV NS5B polymerase.

Eastman, K.J., Parcella, K., Yeung, K.S., Grant-Young, K.A., Zhu, J., Wang, T., Zhang, Z., Yin, Z., Beno, B.R., Sheriff, S., Kish, K., Tredup, J., Jardel, A.G., Halan, V., Ghosh, K., Parker, D., Mosure, K., Fang, H., Wang, Y.K., Lemm, J., Zhuo, X., Hanumegowda, U., Rigat, K., Donoso, M., Tuttle, M., Zvyaga, T., Haarhoff, Z., Meanwell, N.A., Soars, M.G., Roberts, S.B., Kadow, J.F.

(2017) Medchemcomm 8: 796-806

• PubMed: 30108798 
• DOI: https://doi.org/10.1039/c6md00636a
• Primary Citation of Related Structures:  
  5TWM, 5TWN


• PubMed Abstract: 
  

  The development of a series of novel 7-azabenzofurans exhibiting pan-genotype inhibition of HCV NS5B polymerase via binding to the primer grip site is presented. Many challenges, including poor oral bioavailability, high clearance, bioactivation, high human serum shift, and metabolic stability were encountered and overcome through SAR studies. This work culminated in the selection of BMS-986139 ( 43 ) as a preclinical candidate.

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Organizational Affiliation: 

Bristol-Myers Squibb Pharmaceutical Research and Development , Department of Discovery Chemistry and Molecular Technologies , 5 Research Parkway , Wallingford , Connecticut , USA . Email: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.59 kDa 
• Atom Count: 4,814 
• Modelled Residue Count: 559 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5B RNA-dependent RNA POLYMERASE	A	574	Hepatitis C virus JFH-1	Mutation(s): 1  Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1)) Explore Q99IB8  Go to UniProtKB:  Q99IB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7NG	B [auth A]	5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide C28 H29 F N4 O3 WDGCNGHMLOOKQZ-UHFFFAOYSA-N
PE5	G [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
PG4	H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.207 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.687	α = 90
b = 89.816	β = 90
c = 216.745	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references
• Version 1.2: 2018-10-31
  Changes: Data collection, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary