6FKL

Tubulin-TUB015 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.098 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-affinity ligands of the colchicine domain in tubulin based on a structure-guided design.

Bueno, O.Estevez Gallego, J.Martins, S.Prota, A.E.Gago, F.Gomez-SanJuan, A.Camarasa, M.J.Barasoain, I.Steinmetz, M.O.Diaz, J.F.Perez-Perez, M.J.Liekens, S.Priego, E.M.

(2018) Sci Rep 8: 4242-4242

  • DOI: 10.1038/s41598-018-22382-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microtubule-targeting agents that bind at the colchicine-site of tubulin are of particular interest in antitumoral therapy due to their dual mechanism of action as antimitotics and vascular disrupting agents. Cyclohexanediones derivatives have been d ...

    Microtubule-targeting agents that bind at the colchicine-site of tubulin are of particular interest in antitumoral therapy due to their dual mechanism of action as antimitotics and vascular disrupting agents. Cyclohexanediones derivatives have been described as a new family of colchicine-domain binders with an association constant to tubulin similar to that of colchicine. Here, the high-resolution structures of tubulin in complex with cyclohexanediones TUB015 and TUB075 were solved by X-ray crystallography. A detailed analysis of the tubulin-TUB075 interaction by means of computational affinity maps allowed the identification of two additional regions at the binding site that were addressed with the design and synthesis of a new series of cyclohexanediones with a distal 2-substituted benzofurane. These new compounds showed potent antiproliferative activity with IC 50 values in the nM range, arrested cell cycle progression at the G 2 /M phase and induced apoptosis at sub μM concentrations. Moreover, they caused the destruction of a preformed vascular network in vitro and inhibited the migration of endothelial cells at non-toxic concentrations. Finally, these compounds displayed high affinity for tubulin as substantiated by a K b value of 2.87 × 10 8  M -1 which, to the best of our knowledge, represents the highest binding constant measured to date for a colchicine-domain ligand.


    Organizational Affiliation

    Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium.,Department of Biomedical Sciences (Unidad Asociada IQM,CSIC) and Instituto de Investigación Quimica "Andrés M. del Río" (IQAR), University of Alcalá, Unidad Asociada CSIC, 28805 Alcalá de Henares, Madrid, Spain.,University of Basel, Biozentrum, CH-4056, Basel, Switzerland.,Centro de Investigaciones Biológicas (CIB,CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.,Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland.,Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain. empriego@iqm.csic.es.,Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain.




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 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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B, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
DLK
Query on DLK

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B, D
2-{1-[(2-Methoxyphenyl)amino]ethylidene}-5-phenyl-1,3-cyclohexanedione
C21 H21 N O3
VBDYUYVCODLQFF-AKGOGDBKSA-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
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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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: 2.098 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.748α = 90.00
b = 157.764β = 90.00
c = 179.971γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
PHENIXrefinement

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: 2018-03-21
    Type: Initial release