6GJ4

Tubulin-6j complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-activity relationships, biological evaluation and structural studies of novel pyrrolonaphthoxazepines as antitumor agents.

Brindisi, M.Ulivieri, C.Alfano, G.Gemma, S.de Asis Balaguer, F.Khan, T.Grillo, A.Chemi, G.Menchon, G.Prota, A.E.Olieric, N.Lucena-Agell, D.Barasoain, I.Diaz, J.F.Nebbioso, A.Conte, M.Lopresti, L.Magnano, S.Amet, R.Kinsella, P.Zisterer, D.M.Ibrahim, O.O'Sullivan, J.Morbidelli, L.Spaccapelo, R.Baldari, C.Butini, S.Novellino, E.Campiani, G.Altucci, L.Steinmetz, M.O.Brogi, S.

(2018) Eur J Med Chem 162: 290-320

  • DOI: 10.1016/j.ejmech.2018.11.004

  • PubMed Abstract: 
  • Microtubule-targeting agents (MTAs) are a class of clinically successful anti-cancer drugs. The emergence of multidrug resistance to MTAs imposes the need for developing new MTAs endowed with diverse mechanistic properties. Benzoxazepines were recent ...

    Microtubule-targeting agents (MTAs) are a class of clinically successful anti-cancer drugs. The emergence of multidrug resistance to MTAs imposes the need for developing new MTAs endowed with diverse mechanistic properties. Benzoxazepines were recently identified as a novel class of MTAs. These anticancer agents were thoroughly characterized for their antitumor activity, although, their exact mechanism of action remained elusive. Combining chemical, biochemical, cellular, bioinformatics and structural efforts we developed improved pyrrolonaphthoxazepines antitumor agents and their mode of action at the molecular level was elucidated. Compound 6j, one of the most potent analogues, was confirmed by X-ray as a colchicine-site MTA. A comprehensive structural investigation was performed for a complete elucidation of the structure-activity relationships. Selected pyrrolonaphthoxazepines were evaluated for their effects on cell cycle, apoptosis and differentiation in a variety of cancer cells, including multidrug resistant cell lines. Our results define compound 6j as a potentially useful optimized hit for the development of effective compounds for treating drug-resistant tumors.


    Organizational Affiliation

    European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, via Aldo Moro 2, I-53100, Siena, Italy; Istituto Toscano Tumori, University of Siena, via Aldo Moro 2, I-53100, Siena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A, C
451Bos taurusMutation(s): 0 
Find proteins for P81947 (Bos taurus)
Go to UniProtKB:  P81947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-2B chain
B, D
445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Go to Gene View: TUBB2B
Go to UniProtKB:  Q6B856
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Go to UniProtKB:  P63043
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Tubulin tyrosine ligase
F
384Gallus gallusMutation(s): 0 
Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Go to Gene View: TTL
Go to UniProtKB:  E1BQ43
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
EZW
Query on EZW

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Download CCD File 
B, D
5-(quinolin-5-yl)naphtho[2,3-b]pyrrolo[1,2-d][1,4]oxazepin-4-yl acetate
C27 H18 N2 O3
HVSMPYIXZQQOJE-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

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Download CCD File 
F
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.970α = 90.00
b = 157.810β = 90.00
c = 181.220γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_166608

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release