3BSC | pdb_00003bsc

Crystal Structure of HCV NS5B Polymerase with a Novel Pyridazinone Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3BSC/pdb

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


• Deposited: 2007-12-23 Released: 2008-12-23 
• 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: 2.65 Å
• R-Value Free: 
  0.277 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: other

Literature

Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 1: exploration of 7'-substitution of benzothiadiazine.

Zhou, Y., Webber, S.E., Murphy, D.E., Li, L.S., Dragovich, P.S., Tran, C.V., Sun, Z., Ruebsam, F., Shah, A.M., Tsan, M., Showalter, R.E., Patel, R., Li, B., Zhao, Q., Han, Q., Hermann, T., Kissinger, C.R., Lebrun, L., Sergeeva, M.V., Kirkovsky, L.

(2008) Bioorg Med Chem Lett 18: 1413-1418

• PubMed: 18242088 
• DOI: https://doi.org/10.1016/j.bmcl.2008.01.007
• Primary Citation Related Structures: 
  3BR9, 3BSA, 3BSC


• PubMed Abstract: 
  

  5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. The synthesis, structure-activity relationships (SAR), metabolic stability, and structure-based design approach for this new class of compounds are discussed.

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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: 129.63 kDa 
• Atom Count: 8,977 
• 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
2PD	C [auth A], D [auth B]	5-hydroxy-4-(7-methoxy-1,1-dioxido-2H-1,2,4-benzothiadiazin-3-yl)-2-(3-methylbutyl)-6-phenylpyridazin-3(2H)-one C23 H24 N4 O5 S HTTWNUWLEOXVKB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2PD	BindingDB:  3BSC	IC50: 3.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.277 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.336	α = 90
b = 106.55	β = 90
c = 127.273	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
StructureStudio	data collection
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Zhao, Q., Showalter, R.E., Han, Q., Kissinger, C.R.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary