5W2Y

INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 9-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives.

McKimm-Breschkin, J.L.Barrett, S.Pilling, P.A.Hader, S.Watts, A.G.Streltsov, V.A.

(2018) J. Med. Chem. 61: 1921-1933

  • DOI: 10.1021/acs.jmedchem.7b01467
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Competitive inhibitors of the influenza neuraminidase (NA) were discovered almost 20 years ago, with zanamivir and oseltamivir licensed globally. These compounds are based on a transition state analogue of the sialic acid substrate. We recently showe ...

    Competitive inhibitors of the influenza neuraminidase (NA) were discovered almost 20 years ago, with zanamivir and oseltamivir licensed globally. These compounds are based on a transition state analogue of the sialic acid substrate. We recently showed that 5-N-(acetylamino)-2,3,5-trideoxy-2,3-difluoro-d-erythro-β-l-manno-2-nonulopyranosonic acid (DFSA) and its derivatives are also potent inhibitors of the influenza NA. They are mechanism based inhibitors, forming a covalent bond between the C2 of the sugar ring and Y406 in the NA active site, thus inactivating the enzyme. We have now synthesized a series of deoxygenated DFSA derivatives in order to understand the contribution of each hydroxyl in DFSA to binding and inhibition of the influenza NA. We have investigated their relative efficacy in enzyme assays in vitro, in cell culture, and by X-ray crystallography. We found loss of the 8- and 9-OH had the biggest impact on the affinity of binding and antiviral potency.


    Organizational Affiliation

    CSIRO Manufacturing , 343 Royal Parade, Parkville, Victoria 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A
388Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Go to UniProtKB:  P03472
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
9T7
Query on 9T7

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Download CCD File 
A
(2~{R},3~{R},4~{R},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-1,2-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxane-2-carboxylic acid
C11 H17 F2 N O7
PRVRMQAFLBOHCL-GEFXCWNQSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
9TM
Query on 9TM

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Download CCD File 
A
(2~{R},3~{R},4~{R},5~{R})-3-acetamido-2-[(1~{R},2~{R})-1,2-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid
C11 H17 F N O7
DTEWGJXDNGDFKL-IHBVAVKPSA-O
 Ligand Interaction
9T1
Query on 9T1

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Download CCD File 
A
5-(acetylamino)-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid
C11 H16 F N O7
CNGWPEUTMWFBNW-QITVGDPKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.141 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 181.383α = 90.00
b = 181.383β = 90.00
c = 181.383γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
REFMACrefinement
XFITmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Database references