2HWI

HCV NS5B allosteric inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2HWI/pdb

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


• Deposited: 2006-08-01 Released: 2006-11-07 
• Deposition Author(s): Yao, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Structure-based design of a novel thiazolone scaffold as HCV NS5B polymerase allosteric inhibitors.

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

(2006) Bioorg Med Chem Lett 16: 5888-5891

• PubMed: 16934455 
• DOI: https://doi.org/10.1016/j.bmcl.2006.08.056
• Primary Citation of Related Structures:  
  2HWH, 2HWI


• PubMed Abstract: 
  

  A structure-based approach was performed to design a novel thiazolone scaffold as HCV NS5B inhibitors. A focused library was designed and docked by GOLD. One of the top-scored molecules was synthesized and shown to have similar potency to the initial hit. The X-ray complex structure was determined and validated our design rationale.

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Organizational Affiliation: 

Valeant Pharmaceuticals Research and 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: 128.78 kDa 
• Atom Count: 9,173 
• 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
RNA-directed RNA polymerase (NS5B) (p68)	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
VRX	C [auth A], D [auth B]	(2S)-({(5Z)-5-[(5-ETHYL-2-FURYL)METHYLENE]-4-OXO-4,5-DIHYDRO-1,3-THIAZOL-2-YL}AMINO)(4-FLUOROPHENYL)ACETIC ACID C18 H15 F N2 O4 S RNEACARJKXYVND-MZLJFPOFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VRX	BindingDB:  2HWI	IC50: 1.98e+7 (nM) from 1 assay(s)
	PDBBind:  2HWI	IC50: 3000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.997	α = 90
b = 106.585	β = 90
c = 127.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Yao, N.

Revision History  

• Version 1.0: 2006-11-07
  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: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description