6FKJ | pdb_00006fkj

Tubulin-TUB075 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.206 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1038/s41598-018-22382-x
  • Primary Citation Related Structures: 
    6FKJ, 6FKL

  • 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 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
    • Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 265.66 kDa 
  • Atom Count: 18,235 
  • Modeled Residue Count: 2,197 
  • Deposited Residue Count: 2,319 
  • Unique protein chains: 4

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)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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)
Explore Q6B856 
Go to UniProtKB:  Q6B856
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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)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63043
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin tyrosine ligase384Gallus gallusMutation(s): 0 
Gene Names: TTL

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
G [auth A],
S [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP

Query on ACP



Download:Ideal Coordinates CCD File
AA [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
L [auth B],
W [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
DLW

Query on DLW



Download:Ideal Coordinates CCD File
K [auth B],
V [auth D]
(5~{S})-2-[(~{E})-~{N}-(2-ethoxyphenyl)-~{C}-methyl-carbonimidoyl]-3-oxidanyl-5-phenyl-cyclohex-2-en-1-one
C22 H23 N O3
SXTKBCIYVZKDSS-BDFKGGEMSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
Q [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
R [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B],
O [auth B],
U [auth C],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
T [auth C],
X [auth D],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.67α = 90
b = 157.562β = 90
c = 180.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_166608

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description