8R6O | pdb_00008r6o

Tubulin-4AZA2996 complex

PDB DOI: https://doi.org/10.2210/pdb8R6O/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-22 Released: 2024-11-27
Deposition Author(s): Herman, J., Vanstreels, E., Bardiot, D., Prota, A.E., Olieric, N., Gao, L.-J., Vercruysse, T., Daems, T., Waer, M., Herdewijn, P., Louat, T., Steinmetz, M.O., De Jonghe, S., Sprangers, B., Daelemans, D.
Funding Organization(s): Research Foundation - Flanders (FWO), Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.233 (Depositor), 0.231 (DCC)
R-Value Work:
0.208 (Depositor), 0.205 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

3-nitropyridine analogues as novel microtubule-targeting agents.

Herman, J., Vanstreels, E., Bardiot, D., Prota, A.E., Gaillard, N., Gao, L.J., Vercruysse, T., Persoons, L., Daems, T., Waer, M., Herdewijn, P., Louat, T., Steinmetz, M.O., De Jonghe, S., Sprangers, B., Daelemans, D.

(2024) PLoS One 19: e0307153-e0307153

PubMed: 39509402 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0307153
Primary Citation Related Structures:
8R6O

PubMed Abstract:
Microtubule-targeting agents are an important class of anti-cancer drugs; their full potential is however not realized because of significant myelotoxicity and neurotoxicity. We here report 3-nitropyridine analogues as a novel group of microtubule-targeting agents with potent anti-cancer effects against a broad range of cancer types. We show that these 3-nitropyridines induce cell cycle arrest in the G2-M phase and inhibit tubulin polymerization by interacting with tubulin. Determination of the tubulin-4AZA2996 structure by X-ray crystallography demonstrated that this class of compounds binds to the colchicine-site of tubulin. Furthermore, the anti-cancer effect was demonstrated both in vitro and in vivo in a murine heterotopic xenograft model of colon cancer. When administered intravenously, 4AZA2891 effectively inhibited cancer growth. Whereas 3-nitropyridine compounds do not induce myelotoxicity at pharmacological doses, the neurotoxicity associated with microtubule-targeting agents is still present.

Organizational Affiliation

4AZA Biosciences, Leuven, Belgium.

Macromolecule Content

Total Structure Weight: 265.22 kDa
Atom Count: 17,687
Modeled Residue Count: 2,162
Deposited Residue Count: 2,319
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus) Explore A0A8V0Z8P0 Go to UniProtKB: A0A8V0Z8P0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8V0Z8P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain G [auth A]	G [auth A], O [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F] mmCIF format, chain U [auth F]	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain J [auth B] MOL2 format, chain R [auth D] MOL2 format, chain J [auth B] mmCIF format, chain R [auth D] mmCIF format, chain J [auth B]	J [auth B], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain R [auth D]
RME (Subject of Investigation/LOI) Query on RME Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain L [auth B]	L [auth B], T [auth D]	N6-(4-methylpyridin-2-yl)-N2-(2-morpholinoethyl)-3-nitropyridine-2,6-diamine C₁₇ H₂₂ N₆ O₃ OAEWOLLUOVFYIT-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth B] Focus chain T [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth F] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth F] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], P [auth C], S [auth D], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth F]