6BR6 | pdb_00006br6

N2 neuraminidase in complex with a novel antiviral compound

• PDB DOI: https://doi.org/10.2210/pdb6BR6/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus (A/Perth/16/2009(H3N2))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-11-30 Released: 2018-03-07 
• Deposition Author(s): Li, L.H., Ve, T., Pascolutti, M., Hadhazi, A., Bailly, B., Thomson, R.J., Gao, G.F., von Itzstein, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

A Sulfonozanamivir Analogue Has Potent Anti-influenza Virus Activity.

Hadhazi, A., Li, L., Bailly, B., Maggioni, A., Martin, G., Dirr, L., Dyason, J.C., Thomson, R.J., Gao, G.F., Borbas, A., Ve, T., Pascolutti, M., von Itzstein, M.

(2018) ChemMedChem 13: 785-789

• PubMed: 29453852 
• DOI: https://doi.org/10.1002/cmdc.201800092
• Primary Citation Related Structures: 
  6BR5, 6BR6


• PubMed Abstract: 
  

  Influenza virus infection continues to cause significant, often severe, respiratory illness worldwide. A validated target for the development of anti-influenza agents is the virus surface protein sialidase. In the current study, we have discovered a highly potent inhibitor of influenza virus sialidase, based on a novel sialosyl sulfonate template. The synthesised 3-guanidino sialosyl α-sulfonate, a sulfonozanamivir analogue, inhibits viral replication in vitro at the nanomolar level, comparable to that of the anti-influenza drug zanamivir. Using protein X-ray crystallography we show that the sialosyl α-sulfonate template binds within the sialidase active site in a ¹ C ₄ chair conformation. The C1-sulfonate moiety forms crucial and strong-binding interactions with the active site's triarginyl cluster, while the 3-guanidino moiety interacts significantly with conserved active site residues. This sulfonozanamivir analogue provides a new direction in anti-influenza virus drug development.

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Organizational Affiliation: 
• Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia.
Department of Pharmaceutical Chemistry, University of Debrecen, 4032, Debrecen, Hungary.
University of Chinese Academy of Sciences, Beijing, 101408, China.
Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.61 kDa 
• Atom Count: 3,289 
• Modeled Residue Count: 387 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	387	Influenza A virus (A/Perth/16/2009(H3N2))	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for E0UY46 (Influenza A virus) Explore E0UY46  Go to UniProtKB:  E0UY46
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G01760ZU GlyCosmos: G01760ZU GlyGen: G01760ZU

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E3M	G [auth A]	(1R)-4-acetamido-3-amino-1,5-anhydro-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol C10 H20 N2 O8 S XAZGDFCTWHWJMA-IHICSVBISA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.457	α = 90
b = 108.457	β = 90
c = 70.204	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Li, L.H., Ve, T., Pascolutti, M., Hadhazi, A., Bailly, B., Thomson, R.J., Gao, G.F., von Itzstein, M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1071659

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Database references, Source and taxonomy
• Version 1.2: 2018-05-09
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2020-01-08
  Changes: Author supporting evidence
• Version 2.0: 2020-05-13
  Changes: Atomic model, Data collection
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary