9QY7 | pdb_00009qy7

Crystal Structure of 54e bound to CK2a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.208 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9QY7

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Exploiting the Cryptic alpha D Pocket of Casein Kinase 2 alpha (CK2 alpha ) to Deliver Highly Potent and Selective Type 1 Inhibitors.

Glossop, P.A.Brear, P.Wright, S.Flanagan, N.Glossop, M.S.Lane, C.A.L.Butt, R.P.Spring, D.R.Hyvonen, M.Cawkill, D.

(2025) J Med Chem 68: 21587-21614

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01807
  • Primary Citation Related Structures: 
    9QQX, 9QY7

  • PubMed Abstract: 

    Casein kinase 2α (CK2α) is an oncology drug target that acts as a positive regulator of many tumorigenic signaling pathways. We previously reported that CK2α has a unique cryptic binding site, the αD pocket, that offers the potential for inhibitors with improved kinase selectivity. The prototype bivalent molecule CAM4066 ( 6 ) confirmed that improved selectivity could be achieved while binding in both the ATP-binding site and the αD pocket. A drug discovery project to develop a new series of bivalent CK2α inhibitors with increased cell potency and selectivity identified 61f (APL-5125), a highly potent, ATP-competitive CK2α inhibitor with exquisite kinase selectivity and cellular potency. Compound 61f demonstrates in vivo inhibition of p-AKT S129 in tumors (HCT116) following once-daily oral administration and shows a clear PK-PD relationship with unbound drug exposure. 61f has a superior preclinical profile to existing CK2α inhibitors and is currently under evaluation in patients with advanced solid tumors.


  • Organizational Affiliation
    • Sandexis Medicinal Chemistry Ltd, Discovery Park, Ramsgate Road, Sandwich, Kent CT13 9FF, U.K.

Macromolecule Content 

  • Total Structure Weight: 39.71 kDa 
  • Atom Count: 3,190 
  • Modeled Residue Count: 327 
  • Deposited Residue Count: 328 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha328Homo sapiensMutation(s): 4 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.208 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.295α = 90
b = 45.809β = 111.39
c = 63.064γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references