3CVK

Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3CVK/pdb

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


• Deposited: 2008-04-18 Released: 2009-04-21 
• 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: 2.31 Å
• R-Value Free: 0.272 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 

Starting Model: other

Literature

Hexahydro-pyrrolo- and hexahydro-1H-pyrido[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase.

Ruebsam, F., Sun, Z., Ayida, B.K., Webber, S.E., Zhou, Y., Zhao, Q., Kissinger, C.R., Showalter, R.E., Shah, A.M., Tsan, M., Patel, R., Lebrun, L.A., Kamran, R., Sergeeva, M.V., Bartkowski, D.M., Nolan, T.G., Norris, D.A., Kirkovsky, L.

(2008) Bioorg Med Chem Lett 18: 5002-5005

• PubMed: 18722768 
• DOI: https://doi.org/10.1016/j.bmcl.2008.08.017
• Primary Citation of Related Structures:  
  3CVK


• PubMed Abstract: 
  

  Hexahydro-pyrrolo- and hexahydro-1H-pyrido[1,2-b]pyridazin-2-one analogs were discovered as a novel class of inhibitors of genotype 1 HCV NS5B polymerase. Among these, compound 4c displayed potent inhibitory activities in biochemical and replicon assays (IC(50) (1b) <10 nM; EC(50) (1b)=34 nM) as well as good stability towards human liver microsomes (HLM t(1/2) =59 min).

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Organizational Affiliation: 

Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA. [e-mail]

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: 129.71 kDa 
• Atom Count: 9,014 
• Modelled 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
N34	C [auth A], D [auth B]	N-{3-[1-(3,3-Dimethyl-butyl)-4-hydroxy-2-oxo-1,2,4a,5,6,7-hexahydro-pyrrolo[1,2-b]pyridazin-3-yl]-1,1-dioxo-1,2-dihydro -1lambda6-benzo[1,2,4]thiadiazin-7-yl}-methanesulfonamide C21 H29 N5 O6 S2 OCQGEVFPTYSQCK-HNNXBMFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N34	PDBBind:  3CVK	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.272 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.302	α = 90
b = 106.258	β = 90
c = 126.225	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Zhao, Q., Showalter, R.E., Han, Q., Kissinger, C.R.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-04-03
  Changes: Data collection, Refinement description