3G86

Hepatitis C virus polymerase NS5B (BK 1-570) with thiazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3G86/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus (isolate BK)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-11 Released: 2009-09-08 
• Deposition Author(s): Harris, S.F., Ghate, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Non-nucleoside inhibitors of HCV polymerase NS5B. Part 2: Synthesis and structure-activity relationships of benzothiazine-substituted quinolinediones

de Vicente, J., Hendricks, R.T., Smith, D.B., Fell, J.B., Fischer, J., Spencer, S.R., Stengel, P.J., Mohr, P., Robinson, J.E., Blake, J.F., Hilgenkamp, R.K., Yee, C., Adjabeng, G., Elworthy, T.R., Tracy, J., Chin, E., Li, J., Wang, B., Bamberg, J.T., Stephenson, R., Oshiro, C., Harris, S.F., Ghate, M., Leveque, V., Najera, I., Le Pogam, S., Rajyaguru, S., Ao-Ieong, G., Alexandrova, L., Larrabee, S., Brandl, M., Briggs, A., Sukhtankar, S., Farrell, R., Xu, B.

(2009) Bioorg Med Chem Lett 19: 3642-3646

• PubMed: 19457662 
• DOI: https://doi.org/10.1016/j.bmcl.2009.05.004
• Primary Citation of Related Structures:  
  3G86


• PubMed Abstract: 
  

  A new series of benzothiazine-substituted quinolinediones were evaluated as inhibitors of HCV polymerase NS5B. SAR studies on this series revealed a methyl sulfonamide group as a high affinity feature. Analogues with this group showed submicromolar potencies in the HCV cell based replicon assay. Pharmacokinetic and toxicology studies were also performed on a selected compound (34) to evaluate in vivo properties of this new class of inhibitors of HCV NS5B polymerase.

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Organizational Affiliation: 

Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.59 kDa 
• Atom Count: 9,388 
• Modelled Residue Count: 1,115 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	576	Hepatitis C virus (isolate BK)	Mutation(s): 0  Gene Names: POL EC: 2.7.7.48
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663  Go to UniProtKB:  P26663

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T18	C [auth A], E [auth B]	N-{3-[6-fluoro-1-(4-fluorobenzyl)-4-hydroxy-2-oxo-1,2-dihydroquinolin-3-yl]-1,1-dioxido-4H-1,4-benzothiazin-7-yl}methanesulfonamide C25 H19 F2 N3 O6 S2 SNCZSOMZWKLZNB-UHFFFAOYSA-N
NI	D [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.915	α = 90
b = 106.169	β = 90
c = 126.94	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Harris, S.F., Ghate, M.

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description