7YHN | pdb_00007yhn

ANTI-TUMOR AGENT Y48 IN COMPLEX WITH TUBULIN

PDB DOI: https://doi.org/10.2210/pdb7YHN/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Sus scrofa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-14 Released: 2023-07-26
Deposition Author(s): Du, T., Ji, M., Hou, Z., Lin, S., Zhang, J., Wu, D., Zhang, K., Lu, D., Xu, H., Chen, X.
Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.230 (Depositor), 0.227 (DCC)
R-Value Observed:
0.232 (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

Optimization of Benzamide Derivatives as Potent and Orally Active Tubulin Inhibitors Targeting the Colchicine Binding Site.

Lin, S., Du, T., Zhang, J., Wu, D., Tian, H., Zhang, K., Jiang, L., Lu, D., Sheng, L., Li, Y., Ji, M., Chen, X., Xu, H.

(2022) J Med Chem 65: 16372-16391

PubMed: 36511661 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.2c01208
Primary Citation Related Structures:
7YHN

PubMed Abstract:
Targeting the colchicine binding site on tubulin is a promising strategy to develop cancer therapeutics. Herein, we describe our systematic structure-activity relationship studies of benzamide derivatives that lead to an identification of a potent and orally active tubulin inhibitor 48 , which occupied all three zones of the colchicine binding site in the X-ray co-crystal structure, inhibited tubulin polymerization, promoted mitotic blockade and apoptosis, and exhibited significant antiproliferative activities against various cancer cell lines. Compound 48 demonstrated favorable pharmacokinetic profiles, robust in vivo antitumor efficacies, and acceptable safety profiles. Furthermore, 48 overcame drug resistance in the paclitaxel-resistant A549 xenograft model. Collectively, 48 has been advanced into further preclinical evaluation for the development of next-generation microtubule-targeting drugs.

Organizational Affiliation

State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.

Macromolecule Content

Total Structure Weight: 221.64 kDa
Atom Count: 13,868
Modeled Residue Count: 1,810
Deposited Residue Count: 1,944
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin	E	152	Sus scrofa	Mutation(s): 0 Gene Names: LOC100739720, LOC100155126
UniProt
Find proteins for F2Z508 (Sus scrofa) Explore F2Z508 Go to UniProtKB: F2Z508
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2Z508
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 P [auth D] SDF format, chain M [auth C] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain F [auth A]	F [auth A], M [auth C], P [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth C] Focus chain P [auth D]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
IUK (Subject of Investigation/LOI) Query on IUK Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain K [auth B]	K [auth B], R [auth D]	4-methyl-3-[(4-methylphenyl)sulfonylamino]-~{N}-[(6-methylpyridin-3-yl)methyl]benzamide C₂₂ H₂₃ N₃ O₃ S ZKRBQBKMMRYJKN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain R [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth C] N [auth C] O [auth C] G [auth A], H [auth A], L [auth C], N [auth C], O [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D]