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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Discovery and characterization of a novel class of cyclic peptidic compounds inhibiting the assembly of the protein kinase CK2alpha2/beta2 holoenzyme

Werner, C., Eimermacher, S., Lindenblatt, D., Niefind, K., Pietsch, M.

To be published.

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		--