6GMD | pdb_00006gmd

The crystal structure of CK2alpha in complex with compound 3

PDB DOI: https://doi.org/10.2210/pdb6GMD/pdb

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

Deposited: 2018-05-25 Released: 2018-06-06
Deposition Author(s): Brear, P., Iegre, J., North, A., De Fusco, C., Georgiou, K., Lubin, A., Carro, L., Sore, H., Hyvonen, M., Spring, D.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.221 (Depositor), 0.230 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Novel non-ATP competitive small molecules targeting the CK2 alpha / beta interface.

Brear, P., North, A., Iegre, J., Hadje Georgiou, K., Lubin, A., Carro, L., Green, W., Sore, H.F., Hyvonen, M., Spring, D.R.

(2018) Bioorg Med Chem 26: 3016-3020

PubMed: 29759799 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bmc.2018.05.011
Primary Citation Related Structures:
6GIH, 6GMD

PubMed Abstract:
Increased CK2 levels are prevalent in many cancers. Combined with the critical role CK2 plays in many cell-signaling pathways, this makes it a prime target for down regulation to fight tumour growth. Herein, we report a fragment-based approach to inhibiting the interaction between CK2α and CK2β at the α-β interface of the holoenzyme. A fragment, CAM187, with an IC ₅₀ of 44 μM and a molecular weight of only 257 gmol ^-1 has been identified as the most promising compound. Importantly, the lead fragment only bound at the interface and was not observed in the ATP binding site of the protein when co-crystallised with CK2α. The fragment-like molecules discovered in this study represent unique scaffolds to CK2 inhibition and leave room for further optimisation.

Organizational Affiliation

Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK.

Macromolecule Content

Total Structure Weight: 84.97 kDa
Atom Count: 6,033
Modeled Residue Count: 651
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B	352	Homo sapiens	Mutation(s): 1 Gene Names: CSNK2A1, CK2A1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68400
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
A8Q Query on A8Q Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], J [auth B]	[3-chloranyl-4-(2-propan-2-ylphenyl)phenyl]methylazanium C₁₆ H₁₉ Cl N XAFZSQVXSGXDQY-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	C [auth A], F [auth B], G [auth B], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.247 (Depositor), 0.248 (DCC)
R-Value Work: 0.221 (Depositor), 0.230 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.739	α = 90
b = 68.84	β = 90
c = 333.258	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	090340/Z/09/Z
Wellcome Trust	United Kingdom	107714/Z/15/Z

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2018-06-20
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description