8PVO | pdb_00008pvo

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FG5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.253 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PVO

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 Related Structures: 
    8PVO, 8PVP, 8RDK, 9EPV, 9EPW, 9EPX, 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.

Macromolecule Content 

  • Total Structure Weight: 84.02 kDa 
  • Atom Count: 5,839 
  • Modeled Residue Count: 659 
  • Deposited Residue Count: 676 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FW3
(Subject of Investigation/LOI)

Query on FW3



Download:Ideal Coordinates CCD File
CA [auth B],
M [auth A]
2-[1-(1,3-benzothiazol-6-ylsulfonyl)piperidin-4-yl]-~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]ethanamine
C27 H28 Cl N3 O2 S2
VHVPHPDCJZMZGQ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
C [auth A]
D [auth A]
E [auth A]
AA [auth B],
BA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



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

Query on NA



Download:Ideal Coordinates CCD File
EA [auth B],
P [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.253 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.648α = 90
b = 127.648β = 90
c = 123.901γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2024-08-07
    Changes: Database references