4UB7

High-salt structure of protein kinase CK2 catalytic subunit with 4'-carboxy-6,8-bromo-flavonol (FLC26) showing an extreme distortion of the ATP-binding loop combined with a pi-halogen bond


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

A Note of Caution on the Role of Halogen Bonds for Protein Kinase/Inhibitor Recognition Suggested by High- And Low-Salt CK2 alpha Complex Structures.

Guerra, B.Bischoff, N.Bdzhola, V.G.Yarmoluk, S.M.Issinger, O.G.Golub, A.G.Niefind, K.

(2015) Acs Chem.Biol. 10: 1654-1660

  • DOI: 10.1021/acschembio.5b00235
  • Primary Citation of Related Structures:  
  • Also Cited By: 5M56, 5M4U, 5M4I, 5M4F, 5M4C, 5M44

  • PubMed Abstract: 
  • CK2 is a Ser/Thr kinase recruited by tumor cells to avoid cell death. 4'-Carboxy-6,8-dibromo-flavonol (FLC26) is a nanomolar CK2 inhibitor reducing the physiological phosphorylation of CK2 biomarkers and inducing cell death. Its binding mode to the A ...

    CK2 is a Ser/Thr kinase recruited by tumor cells to avoid cell death. 4'-Carboxy-6,8-dibromo-flavonol (FLC26) is a nanomolar CK2 inhibitor reducing the physiological phosphorylation of CK2 biomarkers and inducing cell death. Its binding mode to the ATP site was predicted to depend primarily on noncovalent interactions not comprising halogen bonds. We confirm this by two independent cocrystal structures which additionally show that FLC26 is selective for an open, protein kinase-untypical conformation of the hinge/helix αD region. The structures suggest how the bromo substituents, found previously in lead optimization studies, contribute to the inhibitory efficacy. In this context, one of the complex structures, obtained by crystallization with the kosmotropic salt NaCl, revealed an unconventional π-halogen bond between the 8-bromo substituent of FLC26 and an aromatic side chain which is absent under low-salt conditions. The kosmotropic salt sensitivity of π-halogen bonds is a novel feature which requires attention in structural comparisons and halogen-bond-based explanations.


    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
    • Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2.
      Golub, A.G.,Bdzhola, V.G.,Kyshenia, Y.V.,Sapelkin, V.M.,Prykhod'ko, A.O.,Kukharenko, O.P.,Ostrynska, O.V.,Yarmoluk, S.M.
      (2011) Mol. Cell. Biochem. 356: 107
    • Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme.
      Niefind, K.,Guerra, B.,Ermakowa, I.,Issinger, O.G.
      (2001) EMBO J. 20: 5320


    Organizational Affiliation

    †University of Southern Denmark, Department of Biochemistry and Molecular Biology, Campusvej 55, DK-5230 Odense, Denmark.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3G5
Query on 3G5

Download SDF File 
Download CCD File 
A
4-(6,8-dibromo-3-hydroxy-4-oxo-4H-chromen-2-yl)benzoic acid
C16 H8 Br2 O5
GDOSILZXICLCEI-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.593α = 90.00
b = 72.593β = 90.00
c = 135.513γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyNI643/4-1
National Academy of Science of UkraineUkraine0107U003345

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence, Derived calculations