9QQX | pdb_00009qqx

Crystal Structure of 54k bound to CK2a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QQX

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: 39.66 kDa 
  • Atom Count: 3,033 
  • 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

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I9L
(Subject of Investigation/LOI)

Query on A1I9L



Download:Ideal Coordinates CCD File
B [auth A]5-[2-[4-[[3-aminocarbonyl-5-(trifluoromethyloxy)phenyl]methylamino]butoxy]ethylamino]benzo[c][2,6]naphthyridine-8-carboxamide
C28 H29 F3 N6 O4
BYUOTROFDJYVHI-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.113α = 90
b = 46.304β = 112.12
c = 63.593γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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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