8BGC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00530
  • Primary Citation of 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.


  • Organizational Affiliation

    Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
338Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QIA (Subject of Investigation/LOI)
Query on QIA

Download Ideal Coordinates CCD File 
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
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth B]
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.34α = 90
b = 127.34β = 90
c = 125.731γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Structural Genomics Consortium (SGC)Canada--

Revision History  (Full details and data files)

  • 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