3CWJ | pdb_00003cwj

Crystal structure of hcv ns5b polymerase with a novel pyridazinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3CWJ/pdb

• Classification: TRANSFERASE, VIRAL PROTEIN
• Organism(s): Hepatitis C virus genotype 1b (isolate BK)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-21 Released: 2009-04-21 
• Deposition Author(s): Han, Q., Showalter, R.E., Zhao, Q., Kissinger, C.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.300 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: other

Literature

4-(1,1-Dioxo-1,4-dihydro-1lambda6-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-ones as potent inhibitors of HCV NS5B polymerase

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

(2008) Bioorg Med Chem Lett 18: 4628-4632

• PubMed: 18662878 
• DOI: https://doi.org/10.1016/j.bmcl.2008.07.014
• Primary Citation Related Structures: 
  3CWJ


• PubMed Abstract: 
  

  4-(1,1-Dioxo-1,4-dihydro-1lambda(6)-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-one analogs were discovered as a novel class of inhibitors of HCV NS5B polymerase. Structure-based design led to the identification of compound 3a that displayed potent inhibitory activities in biochemical and replicon assays (1b IC(50)<10 nM; 1b EC(50)=1.1 nM) as well as good stability toward human liver microsomes (HLM t(1/2)>60 min).

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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: 129.76 kDa 
• Atom Count: 8,947 
• 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	N/A	Mutation(s): 0  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
321	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-1,4-benzothiazin-7-yl}methanesulfonamide C22 H24 N4 O6 S3 KLPXSYJOJCQFSY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
321	BindingDB:  3CWJ	IC50: 10 (nM) from 1 assay(s)
		EC50: min: 1.1, max: 11 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.300 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.107	α = 90
b = 106.393	β = 90
c = 126.731	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: 2009-04-21 
Deposition Author(s): Han, Q., Showalter, R.E., Zhao, 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: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary