8BGC | pdb_00008bgc

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with compound 2 (AA-CS-9-003)

• PDB DOI: https://doi.org/10.2210/pdb8BGC/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-27 Released: 2022-11-23 
• Deposition Author(s): Kraemer, A., Axtman, A.D., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): The Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2.

Davis-Gilbert, Z.W., Kramer, A., Dunford, J.E., Howell, S., Senbabaoglu, F., Wells, C.I., Bashore, F.M., Havener, T.M., Smith, J.L., Hossain, M.A., Oppermann, U., Drewry, D.H., Axtman, A.D.

(2023) ACS Med Chem Lett 14: 432-441

• PubMed: 37077385 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00530
• Primary Citation Related Structures: 
  8BGC


• PubMed Abstract: 
  

  Naphthyridine-based inhibitors were synthesized to yield a potent and cell-active inhibitor of casein kinase 2 (CK2). Compound 2 selectively inhibits CK2α and CK2α' when profiled broadly, thereby making it an exquisitely selective chemical probe for CK2. A negative control that is structurally related but lacks a key hinge-binding nitrogen ( 7 ) was designed on the basis of structural studies. Compound 7 does not bind CK2α or CK2α' in cells and demonstrates excellent kinome-wide selectivity. Differential anticancer activity was observed when compound 2 was profiled alongside a structurally distinct CK2 chemical probe: SGC-CK2-1. This naphthyridine-based chemical probe ( 2 ) represents one of the best available small molecule tools with which to interrogate biology mediated by CK2.

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Organizational Affiliation: 
• Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strabe 9, Frankfurt 60438, Germany.
Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strabe 15, Frankfurt 60438, Germany.
Frankfurt Cancer Institute, Paul-Ehrlich-Straße 42-44, Frankfurt 60596, Germany.
Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, United Kingdom.
Oxford Translational Myeloma Centre, University of Oxford, Oxford OX3 7LD, United Kingdom.
UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.28 kDa 
• Atom Count: 5,475 
• Modeled Residue Count: 653 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B	338	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QIA (Subject of Investigation/LOI)	F [auth A], M [auth B]	5-[(phenylmethyl)amino]pyrimido[4,5-c]quinoline-8-carboxylic acid C19 H14 N4 O2 HEVVNKYNJCSHFA-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
QIA	BindingDB:  8BGC	IC50: min: 200, max: 3000 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.34	α = 90
b = 127.34	β = 90
c = 125.731	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Kraemer, A., Axtman, A.D., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
The Structural Genomics Consortium (SGC)	Canada	--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-01-31
  Changes: Refinement description