2IJN | pdb_00002ijn

Isothiazoles as active-site inhibitors of HCV NS5B polymerase

• PDB DOI: https://doi.org/10.2210/pdb2IJN/pdb

• Classification: TRANSCRIPTION,TRANSFERASE
• Organism(s): Hepatitis C virus subtype 1b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-29 Released: 2006-11-28 
• Deposition Author(s): Yan, S., Yao, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.261 (Depositor) 
• R-Value Work: 
  0.222 (Depositor) 

Literature

Isothiazoles as active-site inhibitors of HCV NS5B polymerase

Yan, S., Appleby, T., Gunic, E., Shim, J.H., Tasu, T., Kim, H., Rong, F., Chen, H., Hamatake, R., Wu, J.Z., Hong, Z., Yao, N.

(2007) Bioorg Med Chem Lett 17: 28-33

• PubMed: 17049853 
• DOI: https://doi.org/10.1016/j.bmcl.2006.10.002
• Primary Citation Related Structures: 
  2IJN


• PubMed Abstract: 
  

  Isothiazole analogs were discovered as a novel class of active-site inhibitors of HCV NS5B polymerase. The best compound has an IC(50) of 200 nM and EC(50) of 100 nM, which is a significant improvement over the starting inhibitor (1). The X-ray complex structure of 1 with HCV NS5B was obtained at a resolution of 2.2A, revealing that the inhibitor is covalently linked with Cys 366 of the 'primer-grip'. Furthermore, it makes considerable contacts with the C-terminus, beta-loop, and more importantly, to the active-site of the enzyme. The uniqueness of this binding mode offers a new insight for the rational design of novel inhibitors for HCV NS5B polymerase.

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Organizational Affiliation: 
• Valeant Pharmaceutical Research and Development, 3300 Hyland Ave., Costa Mesa, CA 92626, 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: 128.74 kDa 
• Atom Count: 9,037 
• Modeled Residue Count: 1,120 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase NS5B	A, B	576	Hepatitis C virus subtype 1b	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q99AU2 (Hepatitis C virus genotype 1b) Explore Q99AU2  Go to UniProtKB:  Q99AU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
221	C [auth A], D [auth B]	(2R,3R)-3-{[3,5-BIS(TRIFLUOROMETHYL)PHENYL]AMINO}-2-CYANO-3-THIOXOPROPANAMIDE C12 H9 F6 N3 O S ZTUMRSFHUOBXAC-LHIURRSHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.261 (Depositor) 
• R-Value Work:  0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.507	α = 90
b = 105.272	β = 90
c = 126.458	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Yan, S., Yao, N.

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary