3CDE

Crystal structure of HCV NS5B polymerase with a novel Pyridazinone inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb3CDE/pdb

• Classification: TRANSFERASE
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-02-26 Released: 2009-03-03 
• 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: 2.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 3: Further optimization of the 2-, 6-, and 7'-substituents and initial pharmacokinetic assessments.

Li, L.S., Zhou, Y., Murphy, D.E., Stankovic, N., Zhao, J., Dragovich, P.S., Bertolini, T., Sun, Z., Ayida, B., Tran, C.V., Ruebsam, F., Webber, S.E., Shah, A.M., Tsan, M., Showalter, R.E., Patel, R., Lebrun, L.A., Bartkowski, D.M., Nolan, T.G., Norris, D.A., Kamran, R., Brooks, J., Sergeeva, M.V., Kirkovsky, L., Zhao, Q., Kissinger, C.R.

(2008) Bioorg Med Chem Lett 18: 3446-3455

• PubMed: 18457949 
• DOI: https://doi.org/10.1016/j.bmcl.2008.02.072
• Primary Citation of Related Structures:  
  3CDE


• PubMed Abstract: 
  

5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. Lead optimization led to the discovery of compound 3a, which displayed potent inhibitory activities in biochemical and replicon assays [IC(50) (1b)<10nM; IC(50) (1a)=22 nM; EC(50) (1b)=5nM], good stability toward human liver microsomes (HLM t(1/2)>60 min), and high ratios of liver to plasma concentrations 12h after a single oral administration to rats.

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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: 129.77 kDa 
• Atom Count: 9,210 
• 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	N/A	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
N3H	C [auth A], D [auth B]	N-{3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide C21 H23 N5 O6 S3 UNKTYNIAIAATDF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N3H	BindingDB:  3CDE	IC50: 10 (nM) from 1 assay(s)
		EC50: 5 (nM) from 1 assay(s)
	PDBBind:  3CDE	IC50: 22 (nM) from 1 assay(s)
	Binding MOAD:  3CDE	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.637	α = 90
b = 106.258	β = 90
c = 126.93	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Zhao, Q., Showalter, R.E., Han, Q., Kissinger, C.R.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations