Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129.53 kDa 
• Atom Count: 9544 
• Modelled Residue Count: 1110 
• Deposited Residue Count: 1152 
• Unique protein chains: 1

3H98

Crystal structure of HCV NS5b 1b with (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyrimidine derivative

• PDB DOI: 10.2210/pdb3H98/pdb

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


• Deposited: 2009-04-30 Released: 2009-10-13 
• Deposition Author(s): Wang, G., Lei, H., Wang, X., Das, D., Mackinnon, C., Montalbetti, C.A.G., Mears, R., Gai, X., Bailey, S., Ruhrmund, D., Hooi, L., Misialek, S., Rajagopalan, R., Cheng, R.K.Y., Barker, J.L., Felicetti, B., Stoycheva, A., Buckman, B., Kossen, K., Seiwert, S., Beigelmana, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.274 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

HCV NS5B polymerase inhibitors 2: Synthesis and in vitro activity of (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives.

Wang, G., Lei, H., Wang, X., Das, D., Hong, J., Mackinnon, C.H., Coulter, T.S., Montalbetti, C.A., Mears, R., Gai, X., Bailey, S.E., Ruhrmund, D., Hooi, L., Misialek, S., Rajagopalan, P.T., Cheng, R.K., Barker, J.J., Felicetti, B., Schonfeld, D.L., Stoycheva, A., Buckman, B.O., Kossen, K., Seiwert, S.D., Beigelman, L.

(2009) Bioorg Med Chem Lett 19: 4480-4483

• PubMed: 19500983 
• DOI: 10.1016/j.bmcl.2009.05.022
• Primary Citation of Related Structures:  
  3H98


• PubMed Abstract: 
  

(1,1-Dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives have been investigated as potential anti-HCV drugs. Their synthesis, HCV NS5B polymerase inhibition, and replicon activity are discussed.

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Organizational Affiliation: 

Discovery Research, InterMune, Inc., Brisbane, CA 94005, USA. [e-mail]

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  EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
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
B5P	C [auth A], E [auth B]	N-{3-[5-hydroxy-8-(3-methylbutyl)-7-oxo-7,8-dihydroimidazo[1,2-a]pyrimidin-6-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide C19 H22 N6 O6 S2 HJSHQVOBZCLIRI-UHFFFAOYSA-N
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B5P	PDBBind:  3H98	IC50: 5 (nM) from 1 assay(s)
	Binding MOAD:  3H98	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.274 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.931	α = 90
b = 106.196	β = 90
c = 126.417	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-04-30 
• Released Date: 2009-10-13 
Deposition Author(s): Wang, G., Lei, H., Wang, X., Das, D., Mackinnon, C., Montalbetti, C.A.G., Mears, R., Gai, X., Bailey, S., Ruhrmund, D., Hooi, L., Misialek, S., Rajagopalan, R., Cheng, R.K.Y., Barker, J.L., Felicetti, B., Stoycheva, A., Buckman, B., Kossen, K., Seiwert, S., Beigelmana, L.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance