9FBM | pdb_00009fbm

Structure of human protein kinase CK2 catalytic subunit (CK2alpha, CSNK2A1 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening

PDB DOI: https://doi.org/10.2210/pdb9FBM/pdb

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

Deposited: 2024-05-14 Released: 2025-06-11
Deposition Author(s): Werner, C., Niefind, K., Pietsch, M., Eimermacher, S., Lindenblatt, D.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.239 (Depositor), 0.238 (DCC)
R-Value Work:
0.185 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Discovery and characterization of a novel class of cyclic peptidic compounds inhibiting the subunit interaction of the protein kinase CK2 alpha 2 beta 2 holoenzyme

Werner, C., Eimermacher, S., Lauwers, M., Lindenblatt, D., Seymen, E., Kulko, E., Klein, L., Steinkruger, M., Baumann, R., Salamon, S., Fried, C., Fischer, D., Oder, A., Neuenschwander, M., Goetz, C., Niefind, K., Pietsch, M.

(2026) RSC Chem Biol

DOI: https://doi.org/10.1039/D6CB00095A

Macromolecule Content

Total Structure Weight: 128.63 kDa
Atom Count: 9,450
Modeled Residue Count: 1,009
Deposited Residue Count: 1,062
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B, C	349	Homo sapiens	Mutation(s): 0 Gene Names: CSNK2A1 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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic peptidomimetic compound FMP37	D [auth F], E [auth G], F [auth H]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NIO Query on NIO Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B], R [auth C]	NICOTINIC ACID C₆ H₅ N O₂ PVNIIMVLHYAWGP-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] N [auth B] H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A]	L [auth A], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1ICB Query on A1ICB	D [auth F], E [auth G], F [auth H]	L-PEPTIDE LINKING	C₁₃ H₁₅ Cl N₂ O₃		PRO
SFE Query on SFE	D [auth F], E [auth G], F [auth H]	PEPTIDE LINKING	C₉ H₁₁ N O₂		--