5N9K

Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive, tight-binding dibenzofuran inhibitor TF107 (5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.643 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A pi-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors.

Schnitzler, A.Gratz, A.Bollacke, A.Weyrich, M.Kucklander, U.Wunsch, B.Gotz, C.Niefind, K.Jose, J.

(2018) Pharmaceuticals 11: --

  • DOI: 10.3390/ph11010023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human protein kinase CK2 is an emerging target for neoplastic diseases. Potent lead structures for human CK2 inhibitors are derived from dibenzofuranones. Two new derivatives, 7,9-dichloro-1,2-dihydro-8-hydroxy-4-[(4-methoxyphenylamino)-methylene]dib ...

    Human protein kinase CK2 is an emerging target for neoplastic diseases. Potent lead structures for human CK2 inhibitors are derived from dibenzofuranones. Two new derivatives, 7,9-dichloro-1,2-dihydro-8-hydroxy-4-[(4-methoxyphenylamino)-methylene]dibenzo[ b , d ]furan-3(2 H )-one ( 4a ) and ( E )-1,3-dichloro-6-[(4-methoxyphenylimino)-methyl]dibenzo[ b , d ]furan-2,7-diol ( 5 ) were tested for inhibition of CK2 and induction of apoptosis in LNCaP cells. Both turned out to be tight binding inhibitors, with IC 50 values of 7 nM ( 4a ) and 5 nM ( 5 ) and an apparent K i value of 0.4 nM for both. Compounds 4a and 5 reduced cellular CK2 activity, indicating cell permeability. Cell viability was substantially impaired in LNCaP cells, as well as apoptosis was induced, which was not appearing in non-neoplastic ARPE-19 cells. Co-crystallization of 4a and 5 revealed an unexpected π -halogen bond of the chloro substituent at C9 with the gatekeeper amino acid Phe113, leading to an inverted binding mode in comparison to parent compound 4b , with the Cl at C6 instead, which was co-crystallized as a control. This indicates that the position of the chloro substituent on ring A of the dibenzofuran scaffold is responsible for an inversion of the binding mode that enhances potency.


    Related Citations: 
    • Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
      Ermakova, I.,Boldyreff, B.,Issinger, O.G.,Niefind, K.
      (2003) J. Mol. Biol. 330: 925
    • Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
      Yde, C.W.,Ermakova, I.,Issinger, O.G.,Niefind, K.
      (2005) J. Mol. Biol. 347: 399
    • Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor.
      Niefind, K.,Bischoff, N.,Golub, A.G.,Bdzhola, V.G.,Balanda, A.O.,Prykhod'ko, A.O.,Yarmoluk, S.M.
      (2017) Pharmaceuticals (Basel) 10: --
    • TF--a novel cell-permeable and selective inhibitor of human protein kinase CK2 induces apoptosis in the prostate cancer cell line LNCaP.
      Goetz, C.,Gratz, A.,Kucklaender, U.,Jose, J.
      (2012) Biochim. Biophys. Acta 1820: 970


    Organizational Affiliation

    Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. claudia.goetz@uks.eu.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. joachim.jose@uni-muenster.de.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. wuensch@uni-muenster.de.,Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany. karsten.niefind@uni-koeln.de.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. gratz.andreas@gmail.com.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. Alexander.Schnitzler@posteo.de.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. kucklaen@uni-duesseldorf.de.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. andre.bo@web.de.,Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. michaelweyrich@gmx.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
8QK
Query on 8QK

Download SDF File 
Download CCD File 
A
1,3-bis(chloranyl)-6-[(~{E})-(4-methoxyphenyl)iminomethyl]dibenzofuran-2,7-diol
C20 H13 Cl2 N O4
UWXKHLVNEQUSFY-NUGSKGIGSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.643 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.876α = 90.00
b = 45.670β = 111.14
c = 63.753γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references
  • Version 1.3: 2018-04-25
    Type: Data collection, Database references