3UPH | pdb_00003uph

Synthesis of novel 4,5-dihydrofurano indoles and their evaluation as HCV NS5B polymerase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3UPH/pdb

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


• Deposited: 2011-11-18 Released: 2012-01-25 
• Deposition Author(s): Velazquez, F., Venkataraman, S., Lesburg, C.A., Duca, J.S., Rosenblum, S.B., Kozlowski, J.A., Njoroge, F.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation as HCV NS5B Polymerase Inhibitors.

Velazquez, F., Venkatraman, S., Lesburg, C.A., Duca, J., Rosenblum, S.B., Kozlowski, J.A., Njoroge, F.G.

(2012) Org Lett 14: 556-559

• PubMed: 22220815 
• DOI: https://doi.org/10.1021/ol203177g
• Primary Citation Related Structures: 
  3UPH, 3UPI


• PubMed Abstract: 
  

  The synthesis of substituted 3,4-dihydrofuranoindoles is reported. These new indole compounds were used to synthesize potent HCV NS5B inhibitors. The binding mode of the dihydrofuranoindole-derived inhibitors was established via X-ray crystallographic studies.

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Organizational Affiliation: 
• Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, 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: 129.48 kDa 
• Atom Count: 9,846 
• Modeled Residue Count: 1,121 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed 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
0C1	D [auth A], E [auth B]	6-(2,5-difluorobenzyl)-N-(methylsulfonyl)-8-(2-oxo-1,2-dihydropyridin-3-yl)-3,6-dihydro-2H-furo[2,3-e]indole-7-carboxamide C24 H19 F2 N3 O5 S GPKCKCQUVBOYCV-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.97	α = 90
b = 106.328	β = 90
c = 134.297	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Velazquez, F., Venkataraman, S., Lesburg, C.A., Duca, J.S., Rosenblum, S.B., Kozlowski, J.A., Njoroge, F.G.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-02-01
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary