5W26

INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 4-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1021/acs.jmedchem.7b01467
  • Primary Citation of Related Structures:  
    5W26, 5W2U, 5W2W, 5W2Y

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase388Influenza A virus (A/tern/Australia/G70C/1975(H11N9))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Explore P03472 
Go to UniProtKB:  P03472
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03472
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9SG
Query on 9SG

Download Ideal Coordinates CCD File 
D [auth A](2R,3R,5R,6R)-5-acetamido-2,3-bis(fluoranyl)-6-[(1R,2R)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid
C11 H17 F2 N O7
AHSNGFVNAWRJGS-WNBQUBFESA-N
9VP
Query on 9VP

Download Ideal Coordinates CCD File 
H [auth A]5-acetamido-2,6-anhydro-3,4,5-trideoxy-3-fluoro-D-erythro-L-gluco-nononic acid
C11 H18 F N O7
AUOXJUOLLXNWIV-MMDZMLKVSA-N
9WM
Query on 9WM

Download Ideal Coordinates CCD File 
G [auth A](2~{R},3~{R},5~{R})-3-acetamido-5-fluoranyl-2-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid
C11 H17 F N O7
JMALISIZGRCKCG-VRRGKTLJSA-O
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.139 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.94α = 90
b = 180.94β = 90
c = 180.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
MOLREPphasing
XFITmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-10-21
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description