Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.48 kDa 
• Atom Count: 2988 
• Residue Count: 328 
• Unique protein chains: 1

5MOT

Crystal structure of CK2alpha with ZT0627 bound

• DOI: 10.2210/pdb5MOT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-12-14 Released: 2017-05-24 
• Deposition Author(s): Brear, P., De Fusco, C., Georgiou, K., Iegre, J., Sore, H., Hyvonen, M., Spring, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.227 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

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

• PubMed: 28495381 
• DOI: 10.1016/j.bmc.2017.04.037
• Primary Citation of Related Structures:  
  5MMR, 5MMF, 5MO6, 5MO5, 5MOT, 5MOV, 5MOH, 5MOD, 5MOE, 5MO8


• 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.

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Organizational Affiliation: 

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	328	Homo sapiens	Mutation(s): 4  Gene Names: CSNK2A1, CK2A1 EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens) Explore P68400  Go to UniProtKB:  P68400
NIH Common Fund Data Resources
PHAROS:  P68400 GTEx:  ENSG00000101266

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBD	A	4-HYDROXYBENZAMIDE C7 H7 N O2 QXSAKPUBHTZHKW-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.227 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.994	α = 90
b = 45.353	β = 111.41
c = 63.396	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XPREP	data reduction
XPREP	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-14 
• Released Date: 2017-05-24 
Deposition Author(s): Brear, P., De Fusco, C., Georgiou, K., Iegre, J., Sore, H., Hyvonen, M., Spring, D.

Revision History 

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Data collection, Database references