9SHR | pdb_00009shr

Alpha-Hemolysin of S.aureus (monomer) in complex with the small molecule N-(3-(Diethylamino)propyl)-1-(6-(p-tolyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl)piperidine-4-carboxamide

PDB DOI: https://doi.org/10.2210/pdb9SHR/pdb

Classification: TOXIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-27 Released: 2026-03-04
Deposition Author(s): Lukat, P., Blankenfeldt, W., Broenstrup, M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

An Imidazo[2,1-b][1,3,4]thiadiazole Derivative Inhibits the Virulence Factor alpha-Hemolysin by Blocking the Pullout of Its Stem Domain.

Korotkov, V.S., Lukat, P., Di Lucrezia, R., Shekhar, A., Degenhart, C., Diestel, R., Bilitewski, U., Dinkel, K., Blankenfeldt, W., Bronstrup, M.

(2026) ChemMedChem 21: e202501098-e202501098

PubMed: 41725408 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cmdc.202501098
Primary Citation Related Structures:
9SHR

PubMed Abstract:
Staphylococcus aureus is a major human pathogen responsible for severe infections that necessitate alternative therapeutic strategies. Its key virulence factor α-hemolysin (Hla) mediates host cell damage via pore formation, making it an attractive target for antivirulence interventions. Here, we report the development of a high-throughput cellular assay measuring toxin-induced calcium influx. Its application led to the identification of thiadiazole-based small molecule inhibitors of Hla. Structure-activity relationship studies with 18 analogs led to inhibitors with a cellular potency up to 5.4 µM. X-ray crystallography of Hla in complex with compound 1 revealed that the thiadiazole bound a hydrophobic pocket at the interface of the amino latch and prestem domains, exerting a dual mechanism that blocks stem loop unfolding as well as membrane attachment. These findings introduce thiadiazoles as a novel chemical class of antivirulence therapeutics against S. aureus infections.

Organizational Affiliation

Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.

Macromolecule Content

Total Structure Weight: 36.29 kDa
Atom Count: 2,640
Modeled Residue Count: 289
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-hemolysin	A	304	Staphylococcus aureus	Mutation(s): 0 Gene Names: hly, hla, SAOUHSC_01121
UniProt
Find proteins for Q2G1X0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1X0 Go to UniProtKB: Q2G1X0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G1X0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JN0 (Subject of Investigation/LOI) Query on A1JN0 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{N}-[3-(diethylamino)propyl]-1-[6-(4-methylphenyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl]piperidine-4-carboxamide C₂₄ H₃₄ N₆ O S SQIJMYYLWKQPLM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]