8B7A

Tubulin - maytansinoid - 4 complex

PDB DOI: https://doi.org/10.2210/pdb8B7A/pdb

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

Deposited: 2022-09-29 Released: 2023-08-23
Deposition Author(s): Boiarska, Z., Perez-Pena, H., Abel, A.-C., Marzullo, P., Alvarez-Bernad, B., Bonato, F., Santini, B., Horvath, D., Lucena-Agell, D., Vasile, F., Sironi, M., Diaz, F.J., Steinmetz, M.O., Prota, A.E., Piaraccini, S., Passarella, D.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission, Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.223
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Maytansinol Functionalization: Towards Useful Probes for Studying Microtubule Dynamics.

Boiarska, Z., Perez-Pena, H., Abel, A.C., Marzullo, P., Alvarez-Bernad, B., Bonato, F., Santini, B., Horvath, D., Lucena-Agell, D., Vasile, F., Sironi, M., Diaz, J.F., Prota, A.E., Pieraccini, S., Passarella, D.

(2023) Chemistry 29: e202203431-e202203431

PubMed: 36468686 Search on PubMed
DOI: https://doi.org/10.1002/chem.202203431
Primary Citation of Related Structures:
8B7A, 8B7B, 8B7C

PubMed Abstract:
Maytansinoids are a successful class of natural and semisynthetic tubulin binders, known for their potent cytotoxic activity. Their wider application as cytotoxins and chemical probes to study tubulin dynamics has been held back by the complexity of natural product chemistry. Here we report the synthesis of long-chain derivatives and maytansinoid conjugates. We confirmed that bulky substituents do not impact their high activity or the scaffold's binding mode. These encouraging results open new avenues for the design of new maytansine-based probes.

Organizational Affiliation

Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133, Milan, Italy.

Macromolecule Content

Total Structure Weight: 265.33 kDa
Atom Count: 18,429
Modelled Residue Count: 2,175
Deposited Residue Count: 2,319
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8V0Z8P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q0F (Subject of Investigation/LOI) Query on Q0F Download Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	[(1~{R},2~{R},3~{S},5~{S},6~{S},16~{E},18~{E},20~{R},21~{S})-11-chloranyl-12,20-dimethoxy-2,5,9,16-tetramethyl-21-oxidanyl-8,23-bis(oxidanylidene)-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1^{10,14}.0^{3,5}]hexacosa-10(26),11,13,16,18-pentaen-6-yl] pent-4-enoate C₃₃ H₄₃ Cl N₂ O₉ LEFRLETVDBIZOP-JPOUEXQWSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth C]	G [auth A], Q [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain Q [auth C]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain X [auth F] MOL2 format, chain X [auth F] mmCIF format, chain X [auth F]	X [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain X [auth F] Interactions & Density Focus chain X [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth D] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D]	L [auth B], T [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-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 O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain W [auth E] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth E] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth E]	I [auth A], N [auth B], P [auth B], S [auth C], W [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth E] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth F]	H [auth A] K [auth A] M [auth B] R [auth C] U [auth D] H [auth A], K [auth A], M [auth B], R [auth C], U [auth D], Y [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain Y [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain Y [auth F]