3PHE | pdb_00003phe

HCV NS5B with a bound quinolone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3PHE/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Orthohepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-03 Released: 2010-11-17 
• Deposition Author(s): Somoza, J.R., To, N., Lehoux, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.264 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

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 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: 258.81 kDa 
• Atom Count: 18,015 
• Modeled Residue Count: 2,232 
• Deposited Residue Count: 2,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV encoded nonstructural 5B protein	A, B, C, D	576	Orthohepacivirus hominis	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for D0PY27 (Hepacivirus hominis) Explore D0PY27  Go to UniProtKB:  D0PY27

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C9A	E [auth A], F [auth B], G [auth C], H [auth D]	4-chlorobenzyl 6-fluoro-7-(4-methylpiperazin-1-yl)-1-[4-(methylsulfonyl)benzyl]-4-oxo-1,4-dihydroquinoline-3-carboxylate C30 H29 Cl F N3 O5 S UNFJKYZUZIXOQX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.264 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.751	α = 90
b = 101.972	β = 90
c = 251.087	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
EPMR	phasing
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Somoza, J.R., To, N., Lehoux, I.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations