5TRJ

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 2-{[2-(carboxymethoxy)benzene-1-carbonyl]amino}-3-[(4-chlorophenyl)methoxy]benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb5TRJ/pdb

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-26 Released: 2016-11-30 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Discovery and initial optimization of alkoxyanthranilic acid derivatives as inhibitors of HCV NS5B polymerase.

Parcella, K., Nickel, A., Beno, B.R., Sheriff, S., Wan, C., Wang, Y.K., Roberts, S.B., Meanwell, N.A., Kadow, J.F.

(2017) Bioorg Med Chem Lett 27: 295-298

• PubMed: 27908764 
• DOI: https://doi.org/10.1016/j.bmcl.2016.11.054
• Primary Citation of Related Structures:  
  5TRH, 5TRI, 5TRJ, 5TRK


• PubMed Abstract: 
  

  Alkoxyanthranilic acid derivatives have been identified to inhibit HCV NS5B polymerase, binding in an allosteric site located at the convergence of the palm and thumb regions. Information from co-crystal structures guided the structural design strategy. Ultimately, two independent structural modifications led to a similar shift in binding mode that when combined led to a synergistic improvement in potency and the identification of inhibitors with sub-micromolar HCV NS5B binding potency.

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Organizational Affiliation: 

Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA. Electronic address: [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: 131.06 kDa 
• Atom Count: 8,817 
• Modelled Residue Count: 1,094 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DEPENDENT RNA POLYMERASE	A, B	574	Hepacivirus hominis	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1)) Explore Q9WMX2  Go to UniProtKB:  Q9WMX2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
23E	C [auth A], J [auth B]	(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid C38 H38 N4 O5 HDBNVTWMHMMKNY-XMHGGMMESA-N
7HO	D [auth A], K [auth B]	2-{[2-(carboxymethoxy)benzene-1-carbonyl]amino}-3-[(4-chlorophenyl)methoxy]benzoic acid C23 H18 Cl N O7 UUTYKXCXDYRGKN-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.4	α = 90
b = 91.5	β = 90
c = 232.8	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 1.2: 2017-01-11
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description