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 
  • R-Value Observed: 0.185 

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
  • Primary Citation of Related Structures:  
    6I8Z

  • 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: 

    Boehringer Ingelheim RCV GmbH & Co KG , 1221 Vienna , Austria.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Focal adhesion kinase 1A281Homo sapiensMutation(s): 0 
Gene Names: PTK2, FAK, FAK1
EC: 2.7.10.2
Find proteins for Q05397 (Homo sapiens)
Explore Q05397 
Go to UniProtKB:  Q05397
NIH Common Fund Data Resources
PHAROS  Q05397
GTEx  ENSG00000169398
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H82
Query on H82
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H82IC50:  17   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.05α = 90
b = 77.09β = 90
c = 82.71γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report


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
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-27
    Changes: Data collection, Database references