8B7A

Tubulin - maytansinoid - 4 complex


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 

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Ligand Structure Quality Assessment 


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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

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
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Entity Groups  
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UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chain
B, D
445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
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UniProt GroupQ6B856
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
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UniProt GroupP63043
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin tyrosine ligase384Gallus gallusMutation(s): 0 
Gene Names: TTL
EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus)
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UniProt GroupA0A8V0Z8P0
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q0F (Subject of Investigation/LOI)
Query on Q0F

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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
GTP
Query on GTP

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G [auth A],
Q [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

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X [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP
Query on GDP

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L [auth B],
T [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES
Query on MES

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O [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
IMD
Query on IMD

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J [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CA
Query on CA

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I [auth A],
N [auth B],
P [auth B],
S [auth C],
W [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.271α = 90
b = 158.55β = 90
c = 181.846γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union860070 TubInTrain
Swiss National Science FoundationSwitzerland31003A_166608

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release