9ONZ | pdb_00009onz

Influenza A Virus Group 2 Hemagglutinin (H7, Strain SH13) in Complex with the Potent Small-Molecule Entry Inhibitor SA-67


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanistic insights into the small-molecule inhibition of influenza A virus entry.

Xu, Y.Anirudhan, V.Gaisina, I.N.Du, H.Alqarni, S.Moore, T.W.Caffrey, M.Manicassamy, B.Zhou, T.Rong, L.Xu, K.

(2025) Proc Natl Acad Sci U S A 122: e2503899122-e2503899122

  • DOI: https://doi.org/10.1073/pnas.2503899122
  • Primary Citation of Related Structures:  
    9ONZ, 9OO1

  • PubMed Abstract: 

    Influenza A virus (IAV) is a zoonotic pathogen responsible for seasonal and pandemic flu. The extensive genetic and antigenic diversity within and between IAV phylogenetic groups presents major challenges for developing universal vaccines and broad-spectrum antiviral therapies. Current interventions provide limited protection due to the virus's high mutation rate and capacity for immune evasion. Recent advancements in viral hemagglutinin (HA)-targeting small-molecule entry inhibitors offer a promising avenue to overcome these limitations. Here, we present structural and functional analyses of two group 2 HA-specific small-molecule inhibitors recently identified by our team. Cryogenic electron microscopy (cryo-EM) structures revealed that these inhibitors bind a conserved pocket within the HA stalk, likely interfering with the conformational rearrangements necessary for membrane fusion and viral entry. Structure-guided mutagenesis confirmed the critical roles of key interacting residues and uncovered distinct resistance profiles between the two compounds, as well as in comparison to Arbidol, a previously reported HA inhibitor. Notably, our structural analysis highlights intrinsic barriers to achieving cross-group inhibition with current small-molecule designs. To address this, we propose an alternative strategy for broadening antiviral coverage. Together, these findings provide mechanistic insights into IAV entry inhibition and a foundation for the rational design of next-generation anti-influenza therapeutics.


  • Organizational Affiliation
    • Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1
A, B, C
335Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A8E4VSR8 (Influenza A virus)
Explore A0A8E4VSR8 
Go to UniProtKB:  A0A8E4VSR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8E4VSR8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2
D, E, F
172Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A8E4QKM0 (Influenza A virus)
Explore A0A8E4QKM0 
Go to UniProtKB:  A0A8E4QKM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8E4QKM0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
oligosaccharide
G, H, I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CC2 (Subject of Investigation/LOI)
Query on A1CC2

Download Ideal Coordinates CCD File 
L [auth A],
O [auth B],
T [auth E]
(4R)-N-cyclohexyl-2-(4-fluorophenyl)imidazo[1,2-a]pyrimidin-3-amine
C18 H19 F N4
YJKLSCSCDJRJFZ-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth B]
N [auth B]
P [auth C]
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth E],
U [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-07-16 
  • Deposition Author(s): Xu, Y., Xu, K.

Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references