9FYF | pdb_00009fyf

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with TR06772818


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9FYF

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Strategic Fluorination to Achieve a Potent, Selective, Metabolically Stable, and Orally Bioavailable Inhibitor of CSNK2.

Ong, H.W.Yang, X.Smith, J.L.Taft-Benz, S.Howell, S.Dickmander, R.J.Havener, T.M.Sanders, M.K.Brown, J.W.Counago, R.M.Chang, E.Kramer, A.Moorman, N.J.Heise, M.Axtman, A.D.Drewry, D.H.Willson, T.M.

(2024) Molecules 29

  • DOI: https://doi.org/10.3390/molecules29174158
  • Primary Citation Related Structures: 
    9FYF

  • PubMed Abstract: 

    The host kinase casein kinase 2 (CSNK2) has been proposed to be an antiviral target against β-coronaviral infection. To pharmacologically validate CSNK2 as a drug target in vivo, potent and selective CSNK2 inhibitors with good pharmacokinetic properties are required. Inhibitors based on the pyrazolo[1,5- a ]pyrimidine scaffold possess outstanding potency and selectivity for CSNK2, but bioavailability and metabolic stability are often challenging. By strategically installing a fluorine atom on an electron-rich phenyl ring of a previously characterized inhibitor 1 , we discovered compound 2 as a promising lead compound with improved in vivo metabolic stability. Compound 2 maintained excellent cellular potency against CSNK2, submicromolar antiviral potency, and favorable solubility, and was remarkably selective for CSNK2 when screened against 192 kinases across the human kinome. We additionally present a co-crystal structure to support its on-target binding mode. In vivo, compound 2 was orally bioavailable, and demonstrated modest and transient inhibition of CSNK2, although antiviral activity was not observed, possibly attributed to its lack of prolonged CSNK2 inhibition.


  • Organizational Affiliation
    • Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, USA.

Macromolecule Content 

  • Total Structure Weight: 83.08 kDa 
  • Atom Count: 5,673 
  • Modeled Residue Count: 664 
  • Deposited Residue Count: 676 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase II subunit alphaA [auth B],
B [auth A]
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IG6
(Subject of Investigation/LOI)

Query on A1IG6



Download:Ideal Coordinates CCD File
K [auth B],
O [auth A]
~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-4-fluoranyl-2-[(3~{S})-3-(methylamino)piperidin-1-yl]phenyl]propanamide
C25 H30 F N9 O
OGORXCIJCPHAET-KRWDZBQOSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]
D [auth B]
E [auth B]
F [auth B]
G [auth B]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
L [auth A],
M [auth A],
N [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.184α = 90
b = 127.184β = 90
c = 124.026γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland875510

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references, Structure summary