9HLG | pdb_00009hlg

Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9HLG

This is version 1.1 of the entry. See complete history

Literature

Oseltamivir aziridines are potent influenza neuraminidase inhibitors and imaging agents.

Vriends, M.B.L.Moran, E.Calvelo, M.Hansen, T.Pickles, I.B.Xin, X.Biezeno, M.Armstrong, Z.W.B.Ferraz, M.J.Li, L.Lilley, A.Harvey, R.Filippov, D.V.Liao, Q.Schroder, S.P.van der Marel, G.A.Artola, M.Aerts, J.M.F.G.Blaza, J.N.Codee, J.D.C.Rovira, C.Overkleeft, H.S.Davies, G.J.

(2026) Proc Natl Acad Sci U S A 123: e2504045123-e2504045123

  • DOI: https://doi.org/10.1073/pnas.2504045123
  • Primary Citation Related Structures: 
    9HLG, 9HLH, 9HLI

  • PubMed Abstract: 

    Influenza neuraminidase (NA) is a critical target for seasonal and pandemic antivirals, including the strains of current concern. Current treatments, such as Zanamivir and Oseltamivir, are limited by noncovalent binding and emerging resistance. We hypothesized that Oseltamivir aziridines would unite transition-state mimicry for tight binding, with aziridine-enabled covalent capture of the catalytic tyrosine, thereby supporting both therapy and activity-based quantification. Here, we present oseltamivir-based aziridines, inspired by cyclophellitol chemistry, that act as covalent inhibitors and activity-based probes via an N -acylaziridine warhead. Free-energy calculations, and NMR observations, indicate a 4 H 5 half-chair preference consistent with the NA transition state, and selected analogues inhibit multiple NA subtypes with low nanomolar binding constants. Diverse evidence establishes covalency: time-dependent inactivation, inhibitor washout, intact-mass shifts, MS/MS identification of a tyrosine adduct, and QM/MM reaction profiles, while cryoEM of N1 aligns with the proposed binding mode, revealing an elimination product. The inhibitors demonstrate formidable activity against diverse viral neuraminidases, including H5N1, and further enable imaging and quantification of active NA. With their dual therapeutic and diagnostic potential, these first-in-class inhibitors indeed benefit from transition state mimicry and covalency, and thus offer a powerful platform for antiviral development and neuraminidase imaging, addressing urgent global health needs in influenza treatment and prevention.


  • Organizational Affiliation
    • Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 172.41 kDa 
  • Atom Count: 11,845 
  • Modeled Residue Count: 1,476 
  • Deposited Residue Count: 1,548 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D
387Influenza A virusMutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for C7FH46 (Influenza A virus)
Explore C7FH46 
Go to UniProtKB:  C7FH46
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7FH46
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IVV
(Subject of Investigation/LOI)

Query on A1IVV



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C],
N [auth D]
(3~{S},4~{R},5~{R},6~{R})-4,6-diacetamido-3-azanyl-5-pentan-3-yloxy-cyclohexene-1-carboxylic acid
C16 H27 N3 O5
DQMSSUUCAPUMMT-GBJTYRQASA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C],
O [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
M [auth C],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:
RECONSTRUCTIONRELION5.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references