5N93

TTK kinase domain in complex with TC-Mps1-12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Target Residence Time-Guided Optimization on TTK Kinase Results in Inhibitors with Potent Anti-Proliferative Activity.

Uitdehaag, J.C.M.de Man, J.Willemsen-Seegers, N.Prinsen, M.B.W.Libouban, M.A.A.Sterrenburg, J.G.de Wit, J.J.P.de Vetter, J.R.F.de Roos, J.A.D.M.Buijsman, R.C.Zaman, G.J.R.

(2017) J. Mol. Biol. 429: 2211-2230

  • DOI: 10.1016/j.jmb.2017.05.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The protein kinase threonine tyrosine kinase (TTK; also known as Mps1) is a critical component of the spindle assembly checkpoint and a promising drug target for the treatment of aggressive cancers, such as triple negative breast cancer. While the fi ...

    The protein kinase threonine tyrosine kinase (TTK; also known as Mps1) is a critical component of the spindle assembly checkpoint and a promising drug target for the treatment of aggressive cancers, such as triple negative breast cancer. While the first TTK inhibitors have entered clinical trials, little is known about how the inhibition of TTK with small-molecule compounds affects cellular activity. We studied the selective TTK inhibitor NTRC 0066-0, which was developed in our own laboratory, together with 11 TTK inhibitors developed by other companies, including Mps-BAY2b, BAY 1161909, BAY 1217389 (Bayer), TC-Mps1-12 (Shionogi), and MPI-0479605 (Myrexis). Parallel testing shows that the cellular activity of these TTK inhibitors correlates with their binding affinity to TTK and, more strongly, with target residence time. TTK inhibitors are therefore an example where target residence time determines activity in in vitro cellular assays. X-ray structures and thermal stability experiments reveal that the most potent compounds induce a shift of the glycine-rich loop as a result of binding to the catalytic lysine at position 553. This "lysine trap" disrupts the catalytic machinery. Based on these insights, we developed TTK inhibitors, based on a (5,6-dihydro)pyrimido[4,5-e]indolizine scaffold, with longer target residence times, which further exploit an allosteric pocket surrounding Lys553. Their binding mode is new for kinase inhibitors and can be classified as hybrid Type I/Type III. These inhibitors have very potent anti-proliferative activity that rivals classic cytotoxic therapy. Our findings will open up new avenues for more applications for TTK inhibitors in cancer treatment.


    Organizational Affiliation

    Netherlands Translational Research Center B.V., Kloosterstraat 9, 5349AB Oss, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity protein kinase TTK
A
313Homo sapiensMutation(s): 0 
Gene Names: TTK (MPS1, MPS1L1)
EC: 2.7.12.1
Find proteins for P33981 (Homo sapiens)
Go to Gene View: TTK
Go to UniProtKB:  P33981
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8QE
Query on 8QE

Download SDF File 
Download CCD File 
A
4-[[4-azanyl-6-(~{tert}-butylamino)-5-cyano-pyridin-2-yl]amino]benzamide
C17 H20 N6 O
XDEFNAWAKYQBQY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.100α = 90.00
b = 107.520β = 90.00
c = 112.970γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
Aimlessdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Data collection, Database references
  • Version 1.2: 2017-07-05
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Data collection