8AHM | pdb_00008ahm

Crystal structure of tubulin in complex with C(13)/C(13')-Bis-Desmethyl-Disorazole Z

PDB DOI: https://doi.org/10.2210/pdb8AHM/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-22 Released: 2022-11-16
Deposition Author(s): Oliva, M.A., Diaz, J.F., Altmann, K.H.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Synthesis and Biological Evaluation of C(13)/C(13')-Bis(desmethyl)disorazole Z.

Bold, C.P., Lucena-Agell, D., Oliva, M.A., Diaz, J.F., Altmann, K.H.

(2023) Angew Chem Int Ed Engl 62: e202212190-e202212190

PubMed: 36281761 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202212190
Primary Citation Related Structures:
8AHM

PubMed Abstract:
We describe the total synthesis of the macrodiolide C(13)/C(13')-bis(desmethyl)disorazole Z through double inter-/intramolecular Stille cross-coupling of a monomeric vinyl stannane/vinyl iodide precursor to form the macrocycle. The key step in the synthesis of this precursor was a stereoselective aldol reaction of a formal Evans acetate aldol product with crotonaldehyde. As demonstrated by X-ray crystallography, the binding mode of C(13)/C(13')-bis(desmethyl)disorazole Z to tubulin is virtually identical with that of the natural product disorazole Z. Likewise, C(13)/C(13')-bis(desmethyl)disorazole Z inhibits tubulin assembly with at least the same potency as disorazole Z and it appears to be a more potent cell growth inhibitor.

Organizational Affiliation

Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 270.99 kDa
Atom Count: 17,626
Modeled Residue Count: 2,158
Deposited Residue Count: 2,365
Unique protein chains: 4

Macromolecules

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| 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% 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	189	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

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M5U (Subject of Investigation/LOI) Query on M5U Download:Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	dimethyl 2,2'-((12Z,122Z,4S,6Z,8E,10E,15S,17Z,19E,21E)-2,13-dioxo-3,14-dioxa-1(4,2),12(2,4)-dioxazolacyclodocosaphane-6,8,10,17,19,21-hexaene-4,15-diyl)(2S,2'S,3S,3'S,4E,4'E)-bis(3-hydroxyhex-4-enoate) C₃₈ H₄₂ N₂ O₁₂ ILLJCNVLLYJJLU-RNYWGXLASA-N		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain R [auth C]	G [auth A], R [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain R [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain Y [auth F]	Y [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain Y [auth F] Interactions & Density Focus chain Y [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain V [auth D] MOL2 format, chain L [auth B] MOL2 format, chain V [auth D] mmCIF format, chain L [auth B] mmCIF format, chain V [auth D]	L [auth B], V [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain V [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	N [auth B], O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth C] MOL2 format, chain K [auth A] MOL2 format, chain U [auth C] mmCIF format, chain K [auth A] mmCIF format, chain U [auth C]	K [auth A], U [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth C] Interactions & Density Focus chain K [auth A] Focus chain U [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C]	J [auth A], P [auth B], Q [auth B], T [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Interactions & Density Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth F]	H [auth A], M [auth B], S [auth C], W [auth D], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth F] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth F]