6Q4Q

The Crystal structure of CK2a bound to P2-C4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


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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:  
    6Q38, 6Q4Q

  • 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, 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 ...

    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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alphaA, B327Homo sapiensMutation(s): 1 
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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Stapled peptideC, D8Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEK (Subject of Investigation/LOI)
Query on HEK

Download Ideal Coordinates CCD File 
L [auth C], M [auth D]3-[1-[(2~{S})-2-(2-acetamidoethanoylamino)-3-oxidanylidene-propyl]-1,2,3-triazol-4-yl]-5-[1-[(2~{S})-2-azanyl-3-[[2-[(2-azanyl-2-oxidanylidene-ethyl)amino]-2-oxidanylidene-ethyl]amino]-3-oxidanylidene-propyl]-1,2,3-triazol-4-yl]benzoic acid
C25 H30 N12 O8
YGGHQLWFDQBKHZ-ROUUACIJSA-N
 Ligand Interaction
BEZ
Query on BEZ

Download Ideal Coordinates CCD File 
F [auth A], K [auth B]BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A], H [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.272α = 90
b = 125.221β = 92.6
c = 66.456γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



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