8QQB | pdb_00008qqb

Crystal structure of protein kinase CK2 catalytic subunit in complex with a Dibromo Dihydro Dibenzofuranone derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of 7,9-Dibromo-dihydrodibenzofuran as a Potent Casein Kinase 2 (CK2) Inhibitor: Synthesis, Biological Evaluation, and Structural Studies on E- / Z -Isomers.

Rumler, H.Schmithals, C.Werner, C.Bollacke, A.Aichele, D.Gotz, C.Niefind, K.Wunsch, B.Jose, J.

(2024) Acs Pharmacol Transl Sci 7: 3846-3866

  • DOI: https://doi.org/10.1021/acsptsci.4c00426
  • Primary Citation Related Structures: 
    8QQB

  • PubMed Abstract: 

    The human protein kinase CK2 is a promising target for cancer treatment. Only two CK2 inhibitors have reached clinical trials until today. Among others, a dibenzofuran scaffold has emerged as highly prospective for the development of new CK2 inhibitors. Thirty-three newly synthesized dibenzofuran-based compounds were tested on their inhibitory potential in vitro . 7,9-Dichloro-8-hydroxy-4-[(phenylamino)methylene]-1,2-dihydro-dibenzo[ b , d ]furan-3(4 H )-one ( 12b ) and 7,9-dibromo-8-hydroxy-4-[(phenylamino)methylene]-1,2-dihydro-dibenzo[ b , d ]furan-3(4 H )-one ( 12c ) showed the lowest IC 50 values with 5.8 nM for both. The dibenzofuran-based CK2 inhibitors crossed the cell membrane of LNCaP human prostate carcinoma cells and reduced intracellular CK2 activity. Among 70 kinases from different representative subgroups of the human kinome, CK2 was most strongly inhibited by compound 12c . Co-crystallization of 12c together with CK2α indicated a π-halogen bond of the bromine at position C9 with the gatekeeper amino acid Phe113. CK2α could bind both the E - and Z -isomers of 12c . Our results provide new insights into the structure-activity relationships of dibenzofuran derivatives.


  • Organizational Affiliation
    • University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, Münster 48149, Germany.

Macromolecule Content 

  • Total Structure Weight: 85.25 kDa 
  • Atom Count: 5,909 
  • Modeled Residue Count: 660 
  • Deposited Residue Count: 698 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
349Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WJE
(Subject of Investigation/LOI)

Query on WJE



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]
(4~{Z})-7,9-bis(bromanyl)-8-oxidanyl-4-(phenylazanylmethylidene)-1,2-dihydrodibenzofuran-3-one
C19 H13 Br2 N O3
PWVSFUXHEKWYBC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.242α = 90
b = 128.242β = 90
c = 124.547γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyNI 643/11-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references
  • Version 1.2: 2025-01-01
    Changes: Database references