4MJV | pdb_00004mjv

Influenza Neuraminidase in complex with a novel antiviral compound

• PDB DOI: https://doi.org/10.2210/pdb4MJV/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Influenza A virus (A/duck/Ukraine/1/1963(H3N8))
• Mutation(s): No 


• Deposited: 2013-09-04 Released: 2014-01-15 
• Deposition Author(s): Kerry, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.285 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Serendipitous discovery of a potent influenza virus a neuraminidase inhibitor.

Mohan, S., Kerry, P.S., Bance, N., Niikura, M., Pinto, B.M.

(2014) Angew Chem Int Ed Engl 53: 1076-1080

• PubMed: 24339250 
• DOI: https://doi.org/10.1002/anie.201308142
• Primary Citation Related Structures: 
  4MJU, 4MJV


• PubMed Abstract: 
  

  We have previously reported a potent neuraminidase inhibitor that comprises a carbocyclic analogue of zanamivir in which the hydrophilic glycerol side chain is replaced by the hydrophobic 3-pentyloxy group of oseltamivir. This hybrid inhibitor showed excellent inhibitory properties in the neuraminidase inhibition assay (Ki =0.46 nM; Ki (zanamivir) =0.16 nM) and in the viral replication inhibition assay in cell culture at 10(-8)  M. As part of this lead optimization, we now report a novel spirolactam that shows comparable inhibitory activity in the cell culture assay to that of our lead compound at 10(-7)  M. The compound was discovered serendipitously during the attempted synthesis of the isothiourea derivative of the original candidate. The X-ray crystal structure of the spirolactam in complex with the N8 subtype neuraminidase offers insight into the mode of inhibition.

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Organizational Affiliation: 
• Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A1S6 (Canada) http://www.sfu.ca/chemistry/groups/pinto/

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 43.59 kDa 
• Atom Count: 3,212 
• Modeled Residue Count: 390 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	390	Influenza A virus (A/duck/Ukraine/1/1963(H3N8))	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)) Explore Q07599  Go to UniProtKB:  Q07599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
27V	B [auth A]	(2E,5S,9R,10S)-10-(acetylamino)-2-imino-4-oxo-9-(pentan-3-yloxy)-1-thia-3-azaspiro[4.5]dec-6-ene-7-carboxylic acid C16 H23 N3 O5 S YPLGHUGDNRYXJS-WQGACYEGSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.285 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.744	α = 90
b = 90.744	β = 90
c = 112.002	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Kerry, P.S.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary