3GOL

HCV NS5b polymerase in complex with 1,5 benzodiazepine inhibitor (R)-11d

• PDB DOI: https://doi.org/10.2210/pdb3GOL/pdb

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


• Deposited: 2009-03-19 Released: 2009-06-16 
• Deposition Author(s): Nyanguile, O., De Bondt, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

1,5-Benzodiazepine inhibitors of HCV NS5B polymerase.

McGowan, D., Nyanguile, O., Cummings, M.D., Vendeville, S., Vandyck, K., Van den Broeck, W., Boutton, C.W., De Bondt, H., Quirynen, L., Amssoms, K., Bonfanti, J.F., Last, S., Rombauts, K., Tahri, A., Hu, L., Delouvroy, F., Vermeiren, K., Vandercruyssen, G., Van der Helm, L., Cleiren, E., Mostmans, W., Lory, P., Pille, G., Van Emelen, K., Fanning, G., Pauwels, F., Lin, T.I., Simmen, K., Raboisson, P.

(2009) Bioorg Med Chem Lett 19: 2492-2496

• PubMed: 19342234 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.035
• Primary Citation of Related Structures:  
  3GOL


• PubMed Abstract: 
  

  Optimization through parallel synthesis of a novel series of hepatitis C virus (HCV) NS5B polymerase inhibitors led to the identification of (R)-11-(4-benzyloxy-2-fluorophenyl)-6-hydroxy-3,3-dimethyl-10-(6-methylpyridine-2-carbonyl)-2,3,4,5,10,11-hexahydro-dibenzo[b,e][1,4]diazepin-1-one 11zc and (R)-11-(4-benzyloxy-2-fluorophenyl)-6-hydroxy-3,3-dimethyl-10-(2,5-dimethyloxazol-4-carbonyl)-2,3,4,5,10,11-hexahydro-dibenzo[b,e][1,4]diazepin-1-one 11zk as potent (replicon EC(50)=400nM and 270nM, respectively) and selective (CC(50)>20muM) inhibitors of HCV replication. These data warrant further lead-optimization efforts.

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Organizational Affiliation: 

Tibotec BVBA, Gen. De Wittelaan L11 B3, B-2800 Mechelen, Belgium.

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: 130.57 kDa 
• Atom Count: 8,869 
• Modelled Residue Count: 1,116 
• Deposited Residue Count: 1,162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	581	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
XND	C [auth A], E [auth B]	(11R)-10-acetyl-11-(2,4-dichlorophenyl)-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one C23 H22 Cl2 N2 O3 JJTPPGUNMJMPLY-QFIPXVFZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XND	PDBBind:  3GOL	IC50: 81 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.048	α = 90
b = 106.62	β = 90
c = 134.679	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Nyanguile, O., De Bondt, H.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations