3GNV

HCV NS5B polymerase in complex with 1,5 benzodiazepine inhibitor 1b

• PDB DOI: https://doi.org/10.2210/pdb3GNV/pdb

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


• Deposited: 2009-03-18 Released: 2009-10-20 
• Deposition Author(s): De Bondt, H., Nyanguile, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.234 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of a benzodiazepine scaffold yields a potent allosteric inhibitor of hepatitis C NS5B RNA polymerase.

Vandyck, K., Cummings, M.D., Nyanguile, O., Boutton, C.W., Vendeville, S., McGowan, D., Devogelaere, B., Amssoms, K., Last, S., Rombauts, K., Tahri, A., Lory, P., Hu, L., Beauchamp, D.A., Simmen, K., Raboisson, P.

(2009) J Med Chem 52: 4099-4102

• PubMed: 19507864 
• DOI: https://doi.org/10.1021/jm9005548
• Primary Citation of Related Structures:  
  3GNV, 3GNW


• PubMed Abstract: 
  

  HCV NS5B polymerase, an essential and virus-specific enzyme, is an important target for drug discovery. Using structure-based design, we optimized a 1,5-benzodiazepine NS5B polymerase inhibitor chemotype into a new sulfone-containing scaffold. The design yielded potent inhibitor (S)-4c (K(D) = 0.79 nM), which has approximately 20-fold greater affinity for NS5B than its carbonyl analogue (R)-2c.

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Organizational Affiliation: 

Tibotec BVBA, Generaal de Wittelaan L 11B 3, 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: 130.85 kDa 
• Atom Count: 8,957 
• 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
XNZ	C [auth A], E [auth B]	(11R)-10-acetyl-11-[4-(benzyloxy)-2-chlorophenyl]-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one C30 H29 Cl N2 O4 VZBRCRRODKYBEF-LJAQVGFWSA-N
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.234 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.291	α = 90
b = 107.965	β = 90
c = 133.799	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: 2009-10-20 
Deposition Author(s): De Bondt, H., Nyanguile, O.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description