9OO1 | pdb_00009oo1

Influenza A Virus Group 2 Hemagglutinin (H7, Strain SH13) in Complex with a Potent Small-Molecule Entry Inhibitor ING-16-36


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9OO1

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 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.

Macromolecule Content 

  • Total Structure Weight: 174.8 kDa 
  • Atom Count: 11,775 
  • Modeled Residue Count: 1,470 
  • Deposited Residue Count: 1,530 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1
A, B, C
338Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A8E4VQE2 (Influenza A virus)
Explore A0A8E4VQE2 
Go to UniProtKB:  A0A8E4VQE2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8E4VQE2
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  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 GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
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
A1CC3
(Subject of Investigation/LOI)

Query on A1CC3



Download:Ideal Coordinates CCD File
N [auth B],
Q [auth C],
S [auth D]
(2M,4S)-2-(2-chloropyridin-4-yl)-N-cyclohexyl-5,7-dimethylimidazo[1,2-a]pyrimidin-3-amine
C19 H22 Cl N5
HERNWKUOCFEFTO-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth B]
M [auth B]
O [auth C]
J [auth A],
K [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
T [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: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



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