3H59

Hepatitis C virus polymerase NS5B with thiazine inhibitor 2

• PDB DOI: https://doi.org/10.2210/pdb3H59/pdb

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


• Deposited: 2009-04-21 Released: 2009-09-08 
• Deposition Author(s): Harris, S.F., Ghate, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Non-nucleoside inhibitors of HCV polymerase NS5B. Part 3: synthesis and optimization studies of benzothiazine-substituted tetramic acids

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., Zhao, J., Elworthy, T.R., Tracy, J., Chin, E., Li, J., Lui, A., Wang, B., Oshiro, C., Harris, S.F., Ghate, M., Leveque, V.J., Najera, I., Le Pogam, S., Rajyaguru, S., Ao-Ieong, G., Alexandrova, L., Fitch, B., Brandl, M., Masjedizadeh, M., Wu, S.Y., de Keczer, S., Voronin, T.

(2009) Bioorg Med Chem Lett 19: 5648-5651

• PubMed: 19700319 
• DOI: https://doi.org/10.1016/j.bmcl.2009.08.023
• Primary Citation of Related Structures:  
  3H59


• PubMed Abstract: 
  

  Benzothiazine-substituted tetramic acids were discovered as highly potent non-nucleoside inhibitors of HCV NS5B polymerase. X-ray crystallography studies confirmed the binding mode of these inhibitors with HCV NS5B polymerase. Rational optimization of time dependent inactivation of CYP 3A4 and clearance was accomplished by incorporation of electron-withdrawing groups to the benzothiazine core.

---

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 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: 129.48 kDa 
• Atom Count: 9,582 
• Modelled Residue Count: 1,114 
• 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: NS5B 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H59	C [auth A], D [auth B]	N-{3-[(5S)-5-(1,1-dimethylpropyl)-1-(4-fluoro-3-methylbenzyl)-4-hydroxy-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]-1,1-dioxido-4H-1,4-benzothiazin-7-yl}methanesulfonamide C26 H30 F N3 O6 S2 FIWSMJXHIVIUAK-XMMPIXPASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
H59	PDBBind:  3H59	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.855	α = 90
b = 106.417	β = 90
c = 127.195	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary