6Z84 | pdb_00006z84

CK2 alpha bound to chemical probe SGC-CK2-1 derivative

• PDB DOI: https://doi.org/10.2210/pdb6Z84/pdb

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


• Deposited: 2020-06-02 Released: 2020-07-29 
• Deposition Author(s): Kraemer, A., Wells, C., Drewry, D.H., Pickett, J.E., Axtman, A.D., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.219 (DCC) 

Starting Model: experimental

Literature

Development of a potent and selective chemical probe for the pleiotropic kinase CK2.

Wells, C.I., Drewry, D.H., Pickett, J.E., Tjaden, A., Kramer, A., Muller, S., Gyenis, L., Menyhart, D., Litchfield, D.W., Knapp, S., Axtman, A.D.

(2021) Cell Chem Biol 28: 546-558.e10

• PubMed: 33484635 
• DOI: https://doi.org/10.1016/j.chembiol.2020.12.013
• Primary Citation Related Structures: 
  6Z83, 6Z84


• PubMed Abstract: 
  

  Building on the pyrazolopyrimidine CK2 (casein kinase 2) inhibitor scaffold, we designed a small targeted library. Through comprehensive evaluation of inhibitor selectivity, we identified inhibitor 24 (SGC-CK2-1) as a highly potent and cell-active CK2 chemical probe with exclusive selectivity for both human CK2 isoforms. Remarkably, despite years of research pointing to CK2 as a key driver in cancer, our chemical probe did not elicit a broad antiproliferative phenotype in >90% of >140 cell lines when tested in dose-response. While many publications have reported CK2 functions, CK2 biology is complex and an available high-quality chemical tool such as SGC-CK2-1 will be indispensable in deciphering the relationships between CK2 function and phenotypes.

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Organizational Affiliation: 
• Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA.
Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada; Department of Oncology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA. Electronic address: [e-mail].

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: 82.55 kDa 
• Atom Count: 5,708 
• Modeled Residue Count: 655 
• 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 [auth AAA], B [auth BBB]	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
QB8 (Subject of Investigation/LOI)	H [auth AAA], M [auth BBB]	~{N}-[1-[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]indol-6-yl]ethanamide C20 H17 N7 O DVDLZLUKYIFIOR-UHFFFAOYSA-N
SO4	C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth BBB], N [auth BBB], O [auth BBB], P [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.219 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.352	α = 90
b = 126.352	β = 90
c = 124.514	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Kraemer, A., Wells, C., Drewry, D.H., Pickett, J.E., Axtman, A.D., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references
• Version 1.2: 2021-04-28
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description