8CGZ

tubulin-AB8939 complex

PDB DOI: https://doi.org/10.2210/pdb8CGZ/pdb

Classification: CELL CYCLE
Organism(s): Ovis aries, Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-02-06 Released: 2024-08-14
Deposition Author(s): Varela, P.F., Gigant, B.
Funding Organization(s): Fondation ARC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.235
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Development of AB8939, a Novel Colchicine-like Microtubule Synthetic Destabilizer with the Ability to Overcome Multidrug Resistance

Humbert, M., Letard, S., Neves, M., Siavoshian Jeay, S., Goubard, A., Casteran, N., Rebuffet, E., Hajem, B., Gros, L., Varela, P.F., Gigant, B., Verdier, P., Castellano, R., Colette, Y., Vey, N., Pez, D., Benjahad, A., Moussy, A., Mansfield, C., Dubreuil, P.

To be published.

Macromolecule Content

Total Structure Weight: 220.21 kDa
Atom Count: 14,545
Modelled Residue Count: 1,835
Deposited Residue Count: 1,935
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A, C	451	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWZ0 (Ovis aries) Explore D0VWZ0 Go to UniProtKB: D0VWZ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWZ0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWY9 (Ovis aries) Explore D0VWY9 Go to UniProtKB: D0VWY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWY9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 3 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C]	F [auth A], L [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D]	H [auth B], N [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain H [auth B] Focus chain N [auth D]
UIY (Subject of Investigation/LOI) Query on UIY Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D]	I [auth B], O [auth D]	1-[4-[2-[[5-(ethoxymethyl)-2-methyl-phenyl]amino]-1,3-oxazol-5-yl]phenyl]imidazolidin-2-one C₂₂ H₂₄ N₄ O₃ ZBAFYGYLXHEICJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain O [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D]	J [auth B], K [auth B], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C]	G [auth A], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth C]