5CVF

Crystal Structure of CK2alpha with Compound 5 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Specific inhibition of CK2 alpha from an anchor outside the active site.

Brear, P.De Fusco, C.Hadje Georgiou, K.Francis-Newton, N.J.Stubbs, C.J.Sore, H.F.Venkitaraman, A.R.Abell, C.Spring, D.R.Hyvonen, M.

(2016) Chem Sci 7: 6839-6845

  • DOI: 10.1039/c6sc02335e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The development of selective inhibitors of protein kinases is challenging because of the significant conservation of the ATP binding site. Here, we describe a new mechanism by which the protein kinase CK2α can be selectively inhibited using features ...

    The development of selective inhibitors of protein kinases is challenging because of the significant conservation of the ATP binding site. Here, we describe a new mechanism by which the protein kinase CK2α can be selectively inhibited using features outside the ATP site. We have identified a new binding site for small molecules on CK2α adjacent to the ATP site and behind the αD loop, termed the αD pocket. An elaborated fragment anchored in this site has been linked with a low affinity fragment binding in the ATP site, creating a novel and selective inhibitor (CAM4066) that binds CK2α with a K d of 320 nM and shows significantly improved selectivity compared to other CK2α inhibitors. CAM4066 shows target engagement in several cell lines and similar potency to clinical trial candidate CX4945. Our data demonstrate that targeting a poorly conserved, cryptic pocket allows inhibition of CK2α via a novel mechanism, enabling the development of a new generation of selective CK2α inhibitors.


    Organizational Affiliation

    Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , UK . Email: mh256@cam.ac.uk.,Medical Research Council Cancer Unit , University of Cambridge , Hutchison/MRC Research Centre , Hills Road , Cambridge CB2 0XZ , UK.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
328Homo sapiensMutation(s): 4 
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
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
54Z
Query on 54Z

Download SDF File 
Download CCD File 
A
1-[3-chloro-4-(trifluoromethoxy)phenyl]methanamine
C8 H7 Cl F3 N O
OVFDZNSGNUXERC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.680α = 90.00
b = 45.900β = 111.86
c = 62.900γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references