9EPV

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC333


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting.

Greco, F.A.Kramer, A.Wahl, L.Elson, L.Ehret, T.A.L.Gerninghaus, J.Mockel, J.Muller, S.Hanke, T.Knapp, S.

(2024) Eur J Med Chem 276: 116672-116672

  • DOI: https://doi.org/10.1016/j.ejmech.2024.116672
  • Primary Citation of Related Structures:  
    8PVO, 8PVP, 8RDK, 9EPV, 9EPW, 9EPY, 9EPZ, 9EQ0, 9EQ1

  • PubMed Abstract: 

    Casein kinase-2 (CK2) are serine/threonine kinases with dual co-factor (ATP and GTP) specificity, that are involved in the regulation of a wide variety of cellular functions. Small molecules targeting CK2 have been described in the literature targeting different binding pockets of the kinase with a focus on type I inhibitors such as the recently published chemical probe SGC-CK2-1. In this study, we investigated whether known allosteric inhibitors binding to a pocket adjacent to helix αD could be combined with ATP mimetic moieties defining a novel class of ATP competitive compounds with a unique binding mode. Linking both binding sites requires a chemical linking moiety that would introduce a 90-degree angle between the ATP mimetic ring system and the αD targeting moiety, which was realized using a sulfonamide. The synthesized inhibitors were highly selective for CK2 with binding constants in the nM range and low micromolar activity. While these inhibitors need to be further improved, the present work provides a structure-based design strategy for highly selective CK2 inhibitors.


  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
338Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1CK2A1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H6H (Subject of Investigation/LOI)
Query on A1H6H

Download Ideal Coordinates CCD File 
I [auth A],
R [auth B]
5-[[2-[(3-chloranyl-4-phenyl-phenyl)methylamino]-7-azaspiro[3.5]nonan-7-yl]sulfonyl]-1,3-dimethyl-benzimidazol-2-one
C30 H33 Cl N4 O3 S
VXLVVZOFGXUTDP-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth A]
G [auth A]
J [auth A]
C [auth A],
D [auth A],
F [auth A],
G [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
H [auth A]
Q [auth B]
U [auth B]
V [auth B]
E [auth A],
H [auth A],
Q [auth B],
U [auth B],
V [auth B],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.09α = 90
b = 127.09β = 90
c = 125.969γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland875510

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references
  • Version 1.2: 2024-08-07
    Changes: Database references