6EII

The crystal structure of CK2alpha in complex with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.935 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Second-generation CK2 alpha inhibitors targeting the alpha D pocket.

Iegre, J.Brear, P.De Fusco, C.Yoshida, M.Mitchell, S.L.Rossmann, M.Carro, L.Sore, H.F.Hyvonen, M.Spring, D.R.

(2018) Chem Sci 9: 3041-3049

  • DOI: 10.1039/c7sc05122k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CK2 is a critical cell cycle regulator that also promotes various anti-apoptotic mechanisms. Development of ATP-non-competitive inhibitors of CK2 is a very attractive strategy considering that the ATP binding site is highly conserved among other kina ...

    CK2 is a critical cell cycle regulator that also promotes various anti-apoptotic mechanisms. Development of ATP-non-competitive inhibitors of CK2 is a very attractive strategy considering that the ATP binding site is highly conserved among other kinases. We have previously utilised a pocket outside the active site to develop a novel CK2 inhibitor, CAM4066 . Whilst CAM4066 bound to this new pocket it was also interacting with the ATP site: herein, we describe an example of a CK2α inhibitor that binds completely outside the active site. This second generation αD-site binding inhibitor, compound CAM4712 (IC 50 = 7 μM, GI 50 = 10.0 ± 3.6 μM), has numerous advantages over the previously reported CAM4066 , including a reduction in the number of rotatable bonds, the absence of amide groups susceptible to the action of proteases and improved cellular permeability. Unlike with CAM4066 , there was no need to facilitate cellular uptake by making a prodrug. Moreover, CAM4712 displayed no drop off between its ability to inhibit the kinase in vitro (IC 50 ) and the ability to inhibit cell proliferation (GI 50 ).


    Organizational Affiliation

    R&D Division , Daiichi Sankyo Co., Ltd. , 1-2-58, Hiromachi, Shinagawa-ku , Tokyo 140-8710 , Japan.,Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK . Email: spring@ch.cam.ac.uk.,Department of Biochemistry , University of Cambridge , CB2 1GA , Cambridge , UK . Email: mh256@cam.ac.uk.,Structure Biophysics & FBLG , Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A, B
352Homo sapiensMutation(s): 1 
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
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
B5W
Query on B5W

Download SDF File 
Download CCD File 
A, B
(3-chloranyl-4-phenyl-phenyl)methyl-(3-phenylpropyl)azanium
C22 H23 Cl N
IAHQDSBGJLCLQL-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.935 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 65.918α = 90.00
b = 66.226β = 90.00
c = 333.160γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom090340/Z/09/Z
Wellcome TrustUnited Kingdom107714/Z/15/Z

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references
  • Version 1.2: 2019-10-09
    Type: Data collection, Derived calculations