5SB9

Tubulin-maytansinoid-4a-complex

• PDB DOI: https://doi.org/10.2210/pdb5SB9/pdb
• Deposition Group: G_1002215 ExploreG_1002215

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


• Deposited: 2021-07-20 Released: 2021-12-08 
• Deposition Author(s): Marzullo, P., Boiarska, Z., Perez-Pena, H., Abel, A.-C., Alvarez-Bernad, B., Lucena-Agell, D., Vasile, F., Sironi, M., Steinmetz, M.O., Prota, A.E., Diaz, J.F., Pieraccini, S., Passarella, D.
• Funding Organization(s): H2020-MSCA-ITN-2019

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Maytansinol Derivatives: Side Reactions as a Chance for New Tubulin Binders.

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

(2022) Chemistry 28: e202103520-e202103520

• PubMed: 34788896 
• DOI: https://doi.org/10.1002/chem.202103520
• Primary Citation of Related Structures:  
  5SB8, 5SB9, 5SBA, 5SBB, 5SBC, 5SBD, 5SBE


• PubMed Abstract: 
  

  Maytansinol is a valuable precursor for the preparation of maytansine derivatives (known as maytansinoids). Inspired by the intriguing structure of the macrocycle and the success in targeted cancer therapy of the derivatives, we explored the maytansinol acylation reaction. As a result, we were able to obtain a series of derivatives with novel modifications of the maytansine scaffold. We characterized these molecules by docking studies, by a comprehensive biochemical evaluation, and by determination of their crystal structures in complex with tubulin. The results shed further light on the intriguing chemical behavior of maytansinoids and confirm the relevance of this peculiar scaffold in the scenario of tubulin binders.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 265.26 kDa 
• Atom Count: 17,725 
• Modelled Residue Count: 2,153 
• Deposited Residue Count: 2,319 
• Unique protein chains: 4

Macromolecules

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 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 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 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5IX (Subject of Investigation/LOI)	T [auth D]	(1S,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-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 phenylacetate C36 H43 Cl N2 O9 AONJXIKSEOWSSU-MPCDUNBLSA-N
GTP	G [auth A], N [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	K [auth B], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES	M [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
IMD	Q [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	I [auth A], J [auth A], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth A], L [auth B], O [auth C], S [auth D], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.539	α = 90
b = 156.717	β = 90
c = 181.697	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Marzullo, P., Boiarska, Z., Perez-Pena, H., Abel, A.-C., Alvarez-Bernad, B., Lucena-Agell, D., Vasile, F., Sironi, M., Steinmetz, M.O., Prota, A.E., Diaz, J.F., Pieraccini, S., Passarella, D.

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Funding Organization	Location	Grant Number
H2020-MSCA-ITN-2019	European Union	860070 TUBINTRAIN

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references
• Version 2.0: 2022-03-09
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-05-22
  Changes: Data collection