3HHK

HCV NS5b polymerase complex with a substituted benzothiadizine

• PDB DOI: https://doi.org/10.2210/pdb3HHK/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Hepatitis C virus subtype 1b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-15 Released: 2009-09-08 
• Deposition Author(s): Concha, N.O., Singh, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

Substituted benzothiadizine inhibitors of Hepatitis C virus polymerase.

Shaw, A.N., Tedesco, R., Bambal, R., Chai, D., Concha, N.O., Darcy, M.G., Dhanak, D., Duffy, K.J., Fitch, D.M., Gates, A., Johnston, V.K., Keenan, R.M., Lin-Goerke, J., Liu, N., Sarisky, R.T., Wiggall, K.J., Zimmerman, M.N.

(2009) Bioorg Med Chem Lett 19: 4350-4353

• PubMed: 19515564 
• DOI: https://doi.org/10.1016/j.bmcl.2009.05.091
• Primary Citation of Related Structures:  
  3HHK


• PubMed Abstract: 
  

  The synthesis and optimisation of HCV NS5B polymerase inhibitors with improved potency versus the existing compound 1 is described. Substitution in the benzothiadiazine portion of the molecule, furnishing improvement in potency in the high protein Replicon assay, is highlighted, culminating in the discovery of 12h, a highly potent oxyacetamide derivative.

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Organizational Affiliation: 

Department of Medicinal Chemistry, GlaxoSmithKline, Collegeville, PA 19426, USA.

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: 125.84 kDa 
• Atom Count: 9,302 
• Modelled Residue Count: 1,126 
• Deposited Residue Count: 1,126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS5 polymerase	A, B	563	Hepatitis C virus subtype 1b	Mutation(s): 0
UniProt
Find proteins for Q99AU2 (Hepatitis C virus subtype 1b) Explore Q99AU2  Go to UniProtKB:  Q99AU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
77Z	C [auth A], D [auth B]	2-({(3R)-3-[(3S)-1-(3-methylbutyl)-2,4-dioxo-1,2,3,4-tetrahydroquinolin-3-yl]-1,1-dioxido-3,4-dihydro-2H-1,2,4-benzothiadiazin-7-yl}oxy)acetamide C23 H26 N4 O6 S BIRTVLIYTDXUDJ-IFMALSPDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
77Z	PDBBind:  3HHK	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.74	α = 90
b = 107.442	β = 90
c = 126.807	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Concha, N.O., Singh, O.

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2024-02-21
  Changes: Advisory, Data collection, Database references, Derived calculations