9HYH | pdb_00009hyh

Protein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex with F2X-Entry screen fragment D02 and CX-4945 (Silmitasertib)

PDB DOI: https://doi.org/10.2210/pdb9HYH/pdb

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

Deposited: 2025-01-10 Released: 2026-01-14
Deposition Author(s): Werner, C., Harasimowicz, H., Barthel, T., Weiss, M.S., Niefind, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystallographic Fragment Screening with CK2 alpha', an Isoform of Human Protein Kinase CK2 Catalytic Subunit, and Its Use to Obtain a CK2 alpha'/Heparin Complex Structure

Werner, C., Barthel, T., Harasimowicz, H., Marminon, C., Weiss, M.S., Borgne, M.L., Niefind, K.

(2026) Kinases Phosphatases 4: 1

DOI: https://doi.org/10.3390/kinasesphosphatases4010001

Macromolecule Content

Total Structure Weight: 85.68 kDa
Atom Count: 6,122
Modeled Residue Count: 663
Deposited Residue Count: 710
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B	355	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68400
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3NG Query on 3NG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid C₁₉ H₁₂ Cl N₃ O₂ MUOKSQABCJCOPU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
SY4 (Subject of Investigation/LOI) Query on SY4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	~{N}-[5-azanyl-2,4-bis(fluoranyl)phenyl]propane-1-sulfonamide C₉ H₁₂ F₂ N₂ O₂ S KLZYLFPBFHWHBO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.241 (Depositor), 0.241 (DCC)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.172	α = 90
b = 127.172	β = 90
c = 124.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Aimless	data scaling
autoPROC	data processing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-14

Deposition Author(s):

Harasimowicz, H.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	NI 643/11-1

Revision History (Full details and data files)

Version 1.0: 2026-01-14
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.