5JYY

Structure-based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-resistant Influenza Viruses


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure-Based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-Resistant Influenza Viruses

Fu, L.Bi, Y.Wu, Y.Zhang, S.Qi, J.Li, Y.Lu, X.Zhang, Z.Lv, X.Yan, J.Gao, G.F.Li, X.

(2016) J Med Chem 59: 6303-6312

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00537
  • Primary Citation of Related Structures:  
    5JYY

  • PubMed Abstract: 

    Zanamivir and oseltamivir are principal influenza antiviral drugs that target viral neuraminidase (NA), but resistant viruses containing mutant NAs with diminished drug affinity are increasingly emerging. Using the structural knowledge of both drug-binding sites and their spatial arrangement on the homotetrameric NA, we have developed a tetravalent zanamivir (TZ) molecule that exhibited marked increases in NA binding affinity, inhibition of NA enzyme activity, and in vitro plus in vivo antiviral efficacy over zanamivir. TZ functioned against both human seasonal H3N2 and avian H7N9 viruses, including drug-resistant mutants. Crystal structure of a resistant N9 NA in complex with TZ explained the function, which showed that four zanamivir residues simultaneously bound to all four monomers of NA. The design method of TZ described in this study may be useful to develop drugs or ligands that target proteins with multiple binding sites. The potent anti-influenza activity of TZ makes it attractive for further development.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences , Chaoyang District, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase388Influenza A virusMutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for R4NFR6 (Influenza A virus)
Explore R4NFR6 
Go to UniProtKB:  R4NFR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4NFR6
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)]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
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6PY
Query on 6PY

Download Ideal Coordinates CCD File 
F [auth A]5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-enon ic acid
C16 H27 N5 O9
VAIHIAVLWLNYQQ-IINAIABHSA-N
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.079α = 90
b = 180.079β = 90
c = 180.079γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Ministry of Science and Technology of ChinaChina2012CB518803
National Natural Science Foundation of ChinaChina31470801, 81273381, 21202195, 81301465 and 81330082
Youth Innovation Promotion Association, CASChina2016086

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references
  • Version 1.2: 2016-07-27
    Changes: Database references
  • Version 1.3: 2017-08-16
    Changes: Database references, Derived calculations
  • Version 1.4: 2018-10-24
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary