8R6K | pdb_00008r6k

Crystal structure of Candida glabrata Bdf1 bromodomain 1 bound to a phenyltriazine ligand

PDB DOI: https://doi.org/10.2210/pdb8R6K/pdb

Classification: TRANSCRIPTION
Organism(s): Nakaseomyces glabratus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-22 Released: 2024-10-30
Deposition Author(s): Petosa, C., Wei, K., McKenna, C.E., Govin, J.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential.

Wei, K., Arlotto, M., Overhulse, J.M., Dinh, T.A., Zhou, Y., Dupper, N.J., Yang, J., Kashemirov, B.A., Dawi, H., Garnaud, C., Bourgine, G., Mietton, F., Champleboux, M., Larabi, A., Hayat, Y., Indorato, R.L., Noirclerc-Savoye, M., Skoufias, D., Cornet, M., Rabut, G., McKenna, C.E., Petosa, C., Govin, J.

(2025) Adv Sci (Weinh) 12: e2404260-e2404260

PubMed: 39821709 Search on PubMed
DOI: https://doi.org/10.1002/advs.202404260
Primary Citation Related Structures:
8R6I, 8R6J, 8R6K, 8R6L, 8R6M, 8R6N

PubMed Abstract:
The fungal Bromodomain and Extra-Terminal (BET) protein Bdf1 is a potential antifungal target against invasive fungal infections. However, the need to selectively inhibit both Bdf1 bromodomains (BDs) over human orthologs and the lack of molecular tools to assess on-target antifungal efficacy hamper efforts to develop Bdf1 BD inhibitors as antifungal therapeutics. This study reports a phenyltriazine compound that inhibits both Bdf1 BDs from the human fungal pathogen Candida glabrata with selectivity over the orthologous BDs from the human BET protein Brd4. On-target antifungal activity is established by devising two yeast-based inhibition assays: a growth assay using humanized Candida strains in which the Bdf1 BDs are replaced by their Brd4 counterparts, and a NanoBiT assay that evaluates the BD-mediated association of Bdf1 with chromatin. These assays additionally enable the discovery that BET inhibitor I-BET726 targets both Bdf1 BDs, inhibits the growth of a broad spectrum of Candida species, including antifungal-resistant clinical isolates, and displays efficacy in an invertebrate animal model of infection. These collective findings highlight the promising potential of Bdf1 BD inhibitors as an innovative class of antifungal therapeutics and the pivotal role of yeast-based assay development toward achieving this end.

Organizational Affiliation

Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, 38000, France.

Macromolecule Content

Total Structure Weight: 53.1 kDa
Atom Count: 4,102
Modeled Residue Count: 447
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Candida glabrata strain CBS138 chromosome C complete sequence	A, B, C, D	114	Nakaseomyces glabratus	Mutation(s): 0 Gene Names: CAGL0C02541g
UniProt
Find proteins for Q6FWV7 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FWV7 Go to UniProtKB: Q6FWV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6FWV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y78 (Subject of Investigation/LOI) Query on Y78 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], J [auth C]	6-methyl-~{N}-[(5-methylfuran-2-yl)methyl]-3-(4-methylphenyl)-1,2,4-triazin-5-amine C₁₇ H₁₈ N₄ O FSPDKAUYNLMGSQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], K [auth C], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]