6I8Z

Crystal structure of PTK2 in complex with BI-4464.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Highly Selective PTK2 Proteolysis Targeting Chimeras to Probe Focal Adhesion Kinase Scaffolding Functions.

Popow, J., Arnhof, H., Bader, G., Berger, H., Ciulli, A., Covini, D., Dank, C., Gmaschitz, T., Greb, P., Karolyi-Ozguer, J., Koegl, M., McConnell, D.B., Pearson, M., Rieger, M., Rinnenthal, J., Roessler, V., Schrenk, A., Spina, M., Steurer, S., Trainor, N., Traxler, E., Wieshofer, C., Zoephel, A., Ettmayer, P.

(2019) J.Med.Chem. 62: 2508-2520

  • DOI: 10.1021/acs.jmedchem.8b01826

  • PubMed Abstract: 

    • Focal adhesion tyrosine kinase (PTK2) is often overexpressed in human hepatocellular carcinoma (HCC), and several reports have linked PTK2 depletion and/or pharmacological inhibition to reduced tumorigenicity. However, the clinical relevance of targe ...

    Focal adhesion tyrosine kinase (PTK2) is often overexpressed in human hepatocellular carcinoma (HCC), and several reports have linked PTK2 depletion and/or pharmacological inhibition to reduced tumorigenicity. However, the clinical relevance of targeting PTK2 still remains to be proven. Here, we present two highly selective and functional PTK2 proteolysis-targeting chimeras utilizing von Hippel-Lindau and cereblon ligands to hijack E3 ligases for PTK2 degradation. BI-3663 (cereblon-based) degrades PTK2 with a median DC 50 of 30 nM to >80% across a panel of 11 HCC cell lines. Despite effective PTK2 degradation, these compounds did not phenocopy the reported antiproliferative effects of PTK2 depletion in any of the cell lines tested. By disclosing these compounds, we hope to provide valuable tools for the study of PTK2 degradation across different biological systems.

    Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH Dundee , Scotland, U.K.,Boehringer Ingelheim RCV GmbH & Co KG , 1221 Vienna , Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Focal adhesion kinase 1
A
281Homo sapiensMutation(s): 0 
Gene Names: PTK2 (FAK, FAK1)
EC: 2.7.10.2
Find proteins for Q05397 (Homo sapiens)
Go to Gene View: PTK2
Go to UniProtKB:  Q05397
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H82
Query on H82
Download SDF File 
Download CCD File 
A
3-methoxy-~{N}-(1-methylpiperidin-1-ium-4-yl)-4-[[4-[(3-oxidanylidene-1,2-dihydroinden-4-yl)oxy]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide
C28 H29 F3 N5 O4
QUSSZSMDFABHLI-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.050α = 90.00
b = 77.090β = 90.00
c = 82.710γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2018-11-21 
  • Released Date: 2019-02-20 
  • Deposition Author(s): Bader, G., Zoephel, A.

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Database references
  • Version 1.3: 2019-03-27
    Type: Data collection, Database references