2O5D

Thiazolone-acylsulfonamides as novel HCV NS5B polymerase allosteric inhibitors: Convergence of structure-based drug design and X-ray crystallographic study

• PDB DOI: https://doi.org/10.2210/pdb2O5D/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-05 Released: 2007-02-20 
• Deposition Author(s): Yao, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.206 

Literature

Thiazolone-acylsulfonamides as novel HCV NS5B polymerase allosteric inhibitors: Convergence of structure-based drug design and X-ray crystallographic study.

Yan, S., Appleby, T., Larson, G., Wu, J.Z., Hamatake, R.K., Hong, Z., Yao, N.

(2007) Bioorg Med Chem Lett 17: 1991-1995

• PubMed: 17276060 
• DOI: https://doi.org/10.1016/j.bmcl.2007.01.024
• Primary Citation of Related Structures:  
  2O5D


• PubMed Abstract: 
  

  A novel series of thiazolone-acylsulfonamides were designed as HCV NS5B polymerase allosteric inhibitors. The structure based drug designs (SBDD) were guided by docking results that revealed the potential to explore an additional pocket in the allosteric site. In particular, the designed molecules contain moieties of previously described thiazolone and a newly designed acylsulfonamide linker that is in turn connected with a substituted aromatic ring. The selected compounds were synthesized and demonstrated low muM activity. The X-ray complex structure was determined at a 2.2A resolution and converged with the SBDD principle.

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Organizational Affiliation: 

Valeant Pharmaceutical Research & Development, 3300 Hyland Ave., Costa Mesa, CA 92626, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.14 kDa 
• Atom Count: 9,226 
• Modelled Residue Count: 1,120 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV	A, B	576	Hepacivirus hominis	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
VR1	C [auth A], D [auth B]	(2S)-2-({(5Z)-5-[(5-ETHYL-2-FURYL)METHYLENE]-4-OXO-4,5-DIHYDRO-1,3-THIAZOL-2-YL}AMINO)-2-(4-FLUOROPHENYL)-N-[(4-NITROPHENYL)SULFONYL]ACETAMIDE C24 H19 F N4 O7 S2 RNPVTWTZIDCHEC-MSTPFNHUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VR1	PDBBind:  2O5D	IC50: 7000 (nM) from 1 assay(s)
	Binding MOAD:  2O5D	IC50: 7000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.42	α = 90
b = 105.369	β = 90
c = 126.431	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Yao, N.

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations