3QGH

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-cyclopropyl-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb3QGH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): hepatitis C virus genotype 1a
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-24 Released: 2011-04-20 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase.

Gentles, R.G., Sheriff, S., Beno, B.R., Wan, C., Kish, K., Ding, M., Zheng, X., Chupak, L., Poss, M.A., Witmer, M.R., Morin, P., Wang, Y.K., Rigat, K., Lemm, J., Voss, S., Liu, M., Pelosi, L., Roberts, S.B., Gao, M., Kadow, J.F.

(2011) Bioorg Med Chem Lett 21: 2212-2215

• PubMed: 21441029 
• DOI: https://doi.org/10.1016/j.bmcl.2011.03.011
• Primary Citation of Related Structures:  
  3QGD, 3QGE, 3QGF, 3QGG, 3QGH, 3QGI


• PubMed Abstract: 
  

  Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.

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Organizational Affiliation: 

Bristol Myers Squibb, Chemical and Protein Technologies, Wallingford, CT 06492, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.18 kDa 
• Atom Count: 4,799 
• Modelled Residue Count: 559 
• Deposited Residue Count: 571 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A	571	hepatitis C virus genotype 1a	Mutation(s): 0  Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1)) Explore P26664  Go to UniProtKB:  P26664

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
63F	B [auth A]	N-cyclopropyl-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide C28 H26 F6 N6 O6 S JCQJKQDMSHSQRB-HSZRJFAPSA-N
PO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.3	α = 90
b = 84.7	β = 90
c = 132.9	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description