3IGV | pdb_00003igv

Crystal structure of HCV NS5B polymerase with a novel monocyclic dihydro-pyridinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3IGV/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus (isolate BK)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-28 Released: 2009-12-08 
• Deposition Author(s): Zhao, Q., Showalter, R.E., Han, Q., Kissinger, C.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.301 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: other

Literature

5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase.

Ellis, D.A., Blazel, J.K., Tran, C.V., Ruebsam, F., Murphy, D.E., Li, L.S., Zhao, J., Zhou, Y., McGuire, H.M., Xiang, A.X., Webber, S.E., Zhao, Q., Han, Q., Kissinger, C.R., Lardy, M., Gobbi, A., Showalter, R.E., Shah, A.M., Tsan, M., Patel, R.A., LeBrun, L.A., Kamran, R., Bartkowski, D.M., Nolan, T.G., Norris, D.A., Sergeeva, M.V., Kirkovsky, L.

(2009) Bioorg Med Chem Lett 19: 6047-6052

• PubMed: 19796938 
• DOI: https://doi.org/10.1016/j.bmcl.2009.09.051
• Primary Citation Related Structures: 
  3GYN, 3IGV


• PubMed Abstract: 
  

  The discovery of 5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of the HCV RNA-dependent RNA polymerase (NS5B) is described. Several of these agents also display potent antiviral activity in cell culture experiments (EC50 <0.10 microM). In vitro DMPK data for selected compounds as well as crystal structures of representative inhibitors complexed with the NS5B protein are also disclosed.

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Organizational Affiliation: 
• Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, 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: 129.74 kDa 
• Atom Count: 8,860 
• Modeled Residue Count: 1,114 
• Deposited Residue Count: 1,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DIRECTED RNA POLYMERASE	A, B	578	Hepatitis C virus (isolate BK)	Mutation(s): 1  EC: 2.7.7.48
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
B80	C [auth A], D [auth B]	N-{3-[(6S)-6-ethyl-1-(4-fluorobenzyl)-4-hydroxy-2-oxo-1,2,5,6-tetrahydropyridin-3-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide C22 H23 F N4 O6 S2 GOKCBBJQDMIWKP-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.301 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.911	α = 90
b = 107.217	β = 90
c = 126.214	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
EPMR	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Zhao, Q., Showalter, R.E., Han, Q., Kissinger, C.R.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection
• Version 1.4: 2024-04-03
  Changes: Refinement description