3U4O

Novel HCV NS5B polymerase Inhibitors: Discovery of Indole C2 Acyl sulfonamides

• PDB DOI: https://doi.org/10.2210/pdb3U4O/pdb

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


• Deposited: 2011-10-10 Released: 2011-12-07 
• Deposition Author(s): Anilkumar, G.N., Selyutin, O., Rosenblum, S.B., Zeng, Q., Jiang, Y., Chan, T.-Y., Pu, H., Wang, L., Bennett, F., Chen, K.X., Lesburg, C.A., Duca, J.S., Gavalas, S., Huang, Y., Pinto, P., Sannigrahi, M., Velazquez, F., Venkataraman, S., Vilbubhan, B., Agrawal, S., Ferrari, E., Jiang, C.-K., Huang, H.-C., Shih, N.-Y., Njoroge, F.G., Kozlowski, J.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.196 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

II. Novel HCV NS5B polymerase inhibitors: Discovery of indole C2 acyl sulfonamides.

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

(2012) Bioorg Med Chem Lett 22: 713-717

• PubMed: 22104146 
• DOI: https://doi.org/10.1016/j.bmcl.2011.10.041
• Primary Citation of Related Structures:  
  3U4O, 3U4R


• PubMed Abstract: 
  

  Development of SAR at the C2 position of indole lead 1, a palm site inhibitor of HCV NS5B polymerase (NS5B IC(50)=0.053μM, replicon EC(50)=4.8μM), is described. Initial screening identified an acyl sulfonamide moiety as an isostere for the C2 carboxylic acid group. Further SAR investigation resulted in identification of acyl sufonamide analog 7q (NS5B IC(50)=0.039μM, replicon EC(50)=0.011μM) with >100-fold improved replicon activity.

---

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 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: 129.82 kDa 
• Atom Count: 9,930 
• Modelled Residue Count: 1,121 
• 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 HC-J4	Mutation(s): 0  Gene Names: NS5B 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
08E	C [auth A], E [auth B]	1-[(2-aminopyridin-4-yl)methyl]-5-chloro-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid C20 H15 Cl N4 O3 XPHRQEMVNFKEIN-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
08E	PDBBind:  3U4O	IC50: 53 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.196 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.76	α = 90
b = 106.79	β = 90
c = 133.82	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
autoBUSTER	model building
BUSTER	refinement
autoPROC	data scaling
SCALA	data scaling
autoBUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Anilkumar, G.N., Selyutin, O., Rosenblum, S.B., Zeng, Q., Jiang, Y., Chan, T.-Y., Pu, H., Wang, L., Bennett, F., Chen, K.X., Lesburg, C.A., Duca, J.S., Gavalas, S., Huang, Y., Pinto, P., Sannigrahi, M., Velazquez, F., Venkataraman, S., Vilbubhan, B., Agrawal, S., Ferrari, E., Jiang, C.-K., Huang, H.-C., Shih, N.-Y., Njoroge, F.G., Kozlowski, J.A.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary