5CU2

Crystal structure of CK2alpha with 2-hydroxy-5-methylbenzoic acid and (methyl 4-((3-(3-chloro-4-(phenyl)benzylamino)propyl)amino)-4-oxobutanoat bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066.

De Fusco, C.Brear, P.Iegre, J.Georgiou, K.H.Sore, H.F.Hyvonen, M.Spring, D.R.

(2017) Bioorg Med Chem 25: 3471-3482

  • DOI: https://doi.org/10.1016/j.bmc.2017.04.037
  • Primary Citation of Related Structures:  
    5CT0, 5CTP, 5CU0, 5CU2, 5CX9, 5MMF, 5MMR, 5MO5, 5MO6, 5MO7, 5MO8, 5MOD, 5MOE, 5MOH, 5MOT, 5MOV, 5MOW, 5MP8, 5MPJ

  • PubMed Abstract: 

    Recently we reported the discovery of a potent and selective CK2α inhibitor CAM4066. This compound inhibits CK2 activity by exploiting a pocket located outside the ATP binding site (αD pocket). Here we describe in detail the journey that led to the discovery of CAM4066 using the challenging fragment linking strategy. Specifically, we aimed to develop inhibitors by linking a high-affinity fragment anchored in the αD site to a weakly binding warhead fragment occupying the ATP site. Moreover, we describe the remarkable impact that molecular modelling had on the development of this novel chemical tool. The work described herein shows potential for the development of a novel class of CK2 inhibitors.


  • Organizational Affiliation

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
352Homo 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
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
551
Query on 551

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
J [auth B],
K [auth B]
methyl 3-[(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)amino]-3-oxopropanoate
C20 H23 Cl N2 O3
MTDVIYKGVPWNHL-UHFFFAOYSA-N
54G
Query on 54G

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
2-hydroxy-5-methylbenzoic acid
C8 H8 O3
DLGBEGBHXSAQOC-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
N [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
54G BindingDB:  5CU2 Kd: 5.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.78α = 90
b = 68.257β = 90
c = 334.36γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
BUSTER-TNTrefinement
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

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description