8P05 | pdb_00008p05

Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with Leucettinib-92

PDB DOI: https://doi.org/10.2210/pdb8P05/pdb

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

Deposited: 2023-05-09 Released: 2023-05-17
Deposition Author(s): Kraemer, A., Meijer, L., Knapp, S., Structural Genomics Consortium (SGC)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.255 (Depositor), 0.262 (DCC)
R-Value Work:
0.209 (Depositor), 0.217 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Leucettinibs, a Class of DYRK/CLK Kinase Inhibitors Inspired by the Marine Sponge Natural Product Leucettamine B.

Deau, E., Lindberg, M.F., Miege, F., Roche, D., George, N., George, P., Kramer, A., Knapp, S., Meijer, L.

(2023) J Med Chem 66: 10694-10714

PubMed: 37487467 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.3c00884
Primary Citation Related Structures:
8P04, 8P05

PubMed Abstract:
Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) recently attracted attention due to their central involvement in various pathologies. We here describe a family of DYRK/CLK inhibitors derived from Leucettines and the marine natural product Leucettamine B. Forty-five N 2-functionalized 2-aminoimidazolin-4-ones bearing a fused [6 + 5]-heteroarylmethylene were synthesized. Benzothiazol-6-ylmethylene was selected as the most potent residue among 15 different heteroarylmethylenes. 186 N 2-substituted 2-aminoimidazolin-4-ones bearing a benzothiazol-6-ylmethylene, collectively named Leucettinibs, were synthesized and extensively characterized. Subnanomolar IC ₅₀ (0.5-20 nM on DYRK1A) inhibitors were identified and one Leucettinib was modeled in DYRK1A and co-crystallized with CLK1 and the weaker inhibited off-target CSNK2A1. Kinase-inactive isomers of Leucettinibs (>3-10 μM on DYRK1A), named iso-Leucettinibs, were synthesized and characterized as suitable negative control compounds for functional experiments. Leucettinibs, but not iso-Leucettinibs, inhibit the phosphorylation of DYRK1A substrates in cells. Leucettinibs provide new research tools and potential leads for further optimization toward therapeutic drug candidates.

Organizational Affiliation

Perha Pharmaceuticals, Perharidy, 29680 Roscoff, France.

Macromolecule Content

Total Structure Weight: 82.57 kDa
Atom Count: 5,564
Modeled Residue Count: 657
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B	338	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
WAK (Subject of Investigation/LOI) Query on WAK Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	(4~{Z})-2-(1-adamantylamino)-4-(1,3-benzothiazol-6-ylmethylidene)-1~{H}-imidazol-5-one C₂₁ H₂₂ N₄ O S HEVBCYZPXGZFGS-KDBINBPISA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	C [auth A] D [auth A] E [auth A] G [auth A] H [auth A] C [auth A], D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]