5OSP

The crystal structure of CK2alpha in complex with an analogue of compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A9WClick on this verticalbar to view details

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: https://doi.org/10.1039/c7sc05122k
  • Primary Citation of Related Structures:  
    5OQU, 5ORH, 5ORJ, 5ORK, 5OS7, 5OS8, 5OSL, 5OSP, 5OSR, 5OSU, 5OSZ, 5OT5, 5OT6, 5OTD, 5OTH, 5OTI, 5OTL, 5OTO, 5OTP, 5OTQ, 5OTR, 5OTS, 5OTY, 5OTZ, 5OUE, 5OUL, 5OUM, 5OUU, 5OYF, 6EHK, 6EHU, 6EII

  • 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 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

    Department of Chemistry , University of Cambridge , CB2 1EW , Cambridge , UK . Email: spring@ch.cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha342Homo sapiensMutation(s): 4 
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
ATP
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
A9W (Subject of Investigation/LOI)
Query on A9W

Download Ideal Coordinates CCD File 
G [auth A][3-chloranyl-4-(5-methyl-2-oxidanyl-phenyl)phenyl]methylazanium
C14 H15 Cl N O
NVQGRPSPOJZMIF-UHFFFAOYSA-O
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.632α = 90
b = 45.989β = 112.23
c = 62.757γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XPREPdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A9WClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description