3UDL

3-heterocyclyl quinolone bound to HCV NS5B

• PDB DOI: https://doi.org/10.2210/pdb3UDL/pdb

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


• Deposited: 2011-10-28 Released: 2011-12-21 
• Deposition Author(s): Somoza, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.243 
• R-Value Work: 0.191 
• R-Value Observed: 0.197 

Literature

Quinolones as HCV NS5B polymerase inhibitors.

Kumar, D.V., Rai, R., Brameld, K.A., Somoza, J.R., Rajagopalan, R., Janc, J.W., Xia, Y.M., Ton, T.L., Shaghafi, M.B., Hu, H., Lehoux, I., To, N., Young, W.B., Green, M.J.

(2011) Bioorg Med Chem Lett 21: 82-87

• PubMed: 21145235 
• DOI: https://doi.org/10.1016/j.bmcl.2010.11.068
• Primary Citation of Related Structures:  
  3PHE, 3UDL


• PubMed Abstract: 
  

  Hepatitis C virus (HCV) infection is treated with a combination of peginterferon alfa-2a/b and ribavirin. To address the limitations of this therapy, numerous small molecule agents are in development, which act by directly affecting key steps in the viral life-cycle. Herein we describe our discovery of quinolone derivatives, novel small-molecules that inhibit NS5b polymerase, a key enzyme of the viral life-cycle. A crystal structure of a quinoline analog bound to NS5B reveals that this class of compounds binds to allosteric site-II (non-nucleoside inhibitor-site 2, NNI-2) of this protein.

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Organizational Affiliation: 

Myriad Pharmaceuticals, 305 Chipeta Way, Salt Lake City, UT 84108, 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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 258.8 kDa 
• Atom Count: 18,412 
• Modelled Residue Count: 2,220 
• Deposited Residue Count: 2,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS5B polymerase	A, B, C, D	576	Hepatitis C virus subtype 1b	Mutation(s): 0
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
KLI	E [auth A], F [auth B], G [auth C], H [auth D]	3-(5-benzyl-1,2,4-oxadiazol-3-yl)-6-fluoro-1-[2-fluoro-4-(trifluoromethyl)benzyl]-7-(4-methylpiperazin-1-yl)quinolin-4(1H)-one C31 H26 F5 N5 O2 BZDUJTPAUCQOHN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.243 
• R-Value Work: 0.191 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.746	α = 90
b = 101.863	β = 90
c = 250.867	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Somoza, J.R.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release