6Q38

The Crystal structure of CK2a bound to P1-C4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Efficient development of stable and highly functionalised peptides targeting the CK2 alpha /CK2 beta protein-protein interaction.

Iegre, J.Brear, P.Baker, D.J.Tan, Y.S.Atkinson, E.L.Sore, H.F.O' Donovan, D.H.Verma, C.S.Hyvonen, M.Spring, D.R.

(2019) Chem Sci 10: 5056-5063

  • DOI: 10.1039/c9sc00798a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however ...

    The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117 , prevents the formation of the holoenzyme assembly in vitro , slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be applied to many PPI targets and has the potential to ease the study of PPIs by efficiently providing access to functionalised peptides.


    Organizational Affiliation

    Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK.,Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671.,Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK . Email: mh256@cam.ac.uk.,Oncology, IMED Biotech Unit , AstraZeneca , Cambridge , UK.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551.,Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK . Email: spring@ch.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
327Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Stapled Peptide
C
9Homo sapiensMutation(s): 0 
Gene Names: CSNK2B (CK2N, G5A)
Find proteins for P67870 (Homo sapiens)
Go to Gene View: CSNK2B
Go to UniProtKB:  P67870
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HEK
Query on HEK
C
NON-POLYMERC25 H30 N12 O8

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.887α = 90.00
b = 127.752β = 90.00
c = 54.499γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement

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: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-19
    Type: Data collection, Database references