3SKA

I. Novel HCV NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles

• PDB DOI: https://doi.org/10.2210/pdb3SKA/pdb

• Classification: transferase/transferase INHIBITOR
• Organism(s): Hepatitis C virus isolate HC-J4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-22 Released: 2011-08-31 
• Deposition Author(s): Lesburg, C.A., Anilkumar, G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.194 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

I. Novel HCV NS5B polymerase inhibitors: discovery of indole 2-carboxylic acids with C3-heterocycles.

Anilkumar, G.N., Lesburg, C.A., Selyutin, O., Rosenblum, S.B., Zeng, Q., Jiang, Y., Chan, T.Y., Pu, H., Vaccaro, H., Wang, L., Bennett, F., Chen, K.X., Duca, J., Gavalas, S., Huang, Y., Pinto, P., Sannigrahi, M., Velazquez, F., Venkatraman, S., Vibulbhan, B., Agrawal, S., Butkiewicz, N., Feld, B., Ferrari, E., He, Z., Jiang, C.K., Palermo, R.E., McMonagle, P., Huang, H.C., Shih, N.Y., Njoroge, G., Kozlowski, J.A.

(2011) Bioorg Med Chem Lett 21: 5336-5341

• PubMed: 21840715 
• DOI: https://doi.org/10.1016/j.bmcl.2011.07.021
• Primary Citation of Related Structures:  
  3SKA, 3SKE, 3SKH


• PubMed Abstract: 
  

  SAR development of indole-based palm site inhibitors of HCV NS5B polymerase exemplified by initial indole lead 1 (NS5B IC(50)=0.9 μM, replicon EC(50)>100 μM) is described. Structure-based drug design led to the incorporation of novel heterocyclic moieties at the indole C3-position which formed a bidentate interaction with the protein backbone. SAR development resulted in leads 7q (NS5B IC(50)=0.032 μM, replicon EC(50)=1.4 μM) and 7r (NS5B IC(50)=0.017 μM, replicon EC(50)=0.3 μM) with improved enzyme and replicon activity.

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Organizational Affiliation: 

Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129.33 kDa 
• Atom Count: 9,924 
• Modelled Residue Count: 1,121 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS5B RNA_DEPENDENT RNA POLYMERASE	A, B	576	Hepatitis C virus isolate HC-J4	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4)) Explore O92972  Go to UniProtKB:  O92972

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
053	D [auth A], E [auth B]	1-[(2-aminopyridin-4-yl)methyl]-3-(2-oxo-1,2-dihydropyridin-3-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid C21 H15 F3 N4 O3 CNFSTRPHYZHTGV-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.194 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.67	α = 90
b = 106.97	β = 90
c = 133.74	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Lesburg, C.A., Anilkumar, G.N.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references