4EO8

HCV NS5B polymerase inhibitors: Tri-substituted acylhydrazines as tertiary amide bioisosteres

• PDB DOI: https://doi.org/10.2210/pdb4EO8/pdb

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


• Deposited: 2012-04-13 Released: 2012-06-27 
• Deposition Author(s): Appleby, T.C., Canales, E., Watkins, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Tri-substituted acylhydrazines as tertiary amide bioisosteres: HCV NS5B polymerase inhibitors.

Canales, E., Carlson, J.S., Appleby, T., Fenaux, M., Lee, J., Tian, Y., Tirunagari, N., Wong, M., Watkins, W.J.

(2012) Bioorg Med Chem Lett 22: 4288-4292

• PubMed: 22664130 
• DOI: https://doi.org/10.1016/j.bmcl.2012.05.025
• Primary Citation of Related Structures:  
  4EO6, 4EO8


• PubMed Abstract: 
  

  The use of a tri-substituted acylhydrazine as an isostere of a tertiary amide was explored in a series of HCV NS5B thumb site II inhibitors. Direct replacement generated an analog with similar conformational and physicochemical properties. The series was extended to produce compounds with potent binding affinities and encouraging levels of cellular potency.

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Organizational Affiliation: 

Medicinal Chemistry Department, Gilead Sciences, 333 Lakeside Dr, Foster City, CA 94404, United States. [e-mail]

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: 129.07 kDa 
• Atom Count: 9,837 
• Modelled Residue Count: 1,117 
• Deposited Residue Count: 1,154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	577	Hepatitis C virus (isolate BK)	Mutation(s): 3  Gene Names: NS5B 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
0S3	C [auth A], D [auth B]	5-(3,3-dimethylbut-1-yn-1-yl)-3-{2,2-dimethyl-1-[(trans-4-methylcyclohexyl)carbonyl]hydrazinyl}thiophene-2-carboxylic acid C21 H30 N2 O3 S LATMUSXHHVOIII-SHTZXODSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0S3	PDBBind:  4EO8	Kd: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.59	α = 90
b = 105.93	β = 90
c = 126.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Appleby, T.C., Canales, E., Watkins, W.J.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary