CSNK2A3

Summary

CSNK2A3 (casein kinase 2 alpha 3, HGNC:2458) is a protein-coding gene on chromosome 11p15.4, encoding Casein kinase II subunit alpha 3 (Q8NEV1). Probable catalytic subunit of a constitutively active serine/threonine-protein kinase complex that phosphorylates a large number of substrates containing acidic residues C-terminal to the phosphorylated serine or threonine.

This gene encodes a protein that is highly similar to the casein kinase II alpha protein. Casein kinase II is a serine/threonine protein kinase complex that phosphorylates numerous substrates including casein. The alpha subunit is the catalytic component of the complex. Mutations in this gene may be associated with a susceptibility to lung cancer. There are contradictory views among published reports of this gene as to whether or not it is a protein-coding gene or a processed pseudogene (PMIDs: 20625391, 20625391 and 10094393).

Source: NCBI Gene 283106 — RefSeq curated summary.

At a glance

• Druggable target: yes — 11 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_001256686

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2458
Approved symbol	CSNK2A3
Name	casein kinase 2 alpha 3
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000254598
Ensembl biotype	protein_coding
Entrez	283106

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000528848

RefSeq mRNA: 1 — MANE Select: NM_001256686 NM_001256686

CCDS: CCDS59224

Canonical transcript exons

ENST00000528848 — 1 exons

Exon	Start	End
ENSE00002196929	11351942	11353250

Expression profiles

Bgee: expression breadth broad, 73 present calls, max score 80.43.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6323 / max 84.5843, expressed in 315 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118678	0.6323	315

Top tissues by expression

102 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.43	gold quality
calcaneal tendon	UBERON:0003701	51.10	gold quality
colonic epithelium	UBERON:0000397	49.66	gold quality
cortical plate	UBERON:0005343	48.60	gold quality
smooth muscle tissue	UBERON:0001135	46.99	gold quality
right lung	UBERON:0002167	46.30	gold quality
muscle tissue	UBERON:0002385	42.30	gold quality
upper lobe of left lung	UBERON:0008952	42.13	gold quality
duodenum	UBERON:0002114	41.76	gold quality
skeletal muscle tissue	UBERON:0001134	41.58	gold quality
lung	UBERON:0002048	41.54	gold quality
ventricular zone	UBERON:0003053	41.50	gold quality
ganglionic eminence	UBERON:0004023	40.85	gold quality
right lobe of thyroid gland	UBERON:0001119	40.04	silver quality
liver	UBERON:0002107	39.53	gold quality
granulocyte	CL:0000094	39.32	gold quality
placenta	UBERON:0001987	39.17	gold quality
prefrontal cortex	UBERON:0000451	38.75	gold quality
superior frontal gyrus	UBERON:0002661	38.67	gold quality
bone marrow cell	CL:0002092	38.61	gold quality
tonsil	UBERON:0002372	38.50	gold quality
sural nerve	UBERON:0015488	38.11	gold quality
kidney	UBERON:0002113	37.21	gold quality
myometrium	UBERON:0001296	37.19	gold quality
thyroid gland	UBERON:0002046	37.13	gold quality
hindlimb stylopod muscle	UBERON:0004252	37.13	silver quality
muscle of leg	UBERON:0001383	36.33	silver quality
cortex of kidney	UBERON:0001225	36.30	silver quality
right atrium auricular region	UBERON:0006631	36.22	gold quality
gastrocnemius	UBERON:0001388	35.84	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.69

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	csnk2a4	ENSDARG00000091702
mus_musculus	Csnk2a1	ENSMUSG00000074698
rattus_norvegicus	Csnk2a1	ENSRNOG00000005276
drosophila_melanogaster	CkIIalpha	FBGN0264492
caenorhabditis_elegans	kin-3	WBGENE00002191

Paralogs (2): CSNK2A2 (ENSG00000070770), CSNK2A1 (ENSG00000101266)

Protein

Protein identifiers

Casein kinase II subunit alpha 3 — Q8NEV1 (reviewed: Q8NEV1)

Alternative names: Casein kinase II alpha 1 polypeptide pseudogene

All UniProt accessions (1): Q8NEV1

UniProt curated annotations — full annotation on UniProt →

Function. Probable catalytic subunit of a constitutively active serine/threonine-protein kinase complex that phosphorylates a large number of substrates containing acidic residues C-terminal to the phosphorylated serine or threonine. Amplification-dependent oncogene; promotes cell proliferation and tumorigenesis by down-regulating expression of the tumor suppressor protein, PML. May play a role in the pathogenesis of the lung cancer development and progression.

Subunit / interactions. Heterotetramer composed of two catalytic subunits (alpha chain and/or alpha’ chain) and two regulatory subunits (beta chains). Interacts with PML.

Tissue specificity. Detected in blood platelets and megakaryocyte cell lines. Poorly expressed in lung. Highly expressed in lung tumor tissues.

Similarity. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. CK2 subfamily.

RefSeq proteins (1): NP_001243615* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000719	Prot_kinase_dom	Domain
IPR008271	Ser/Thr_kinase_AS	Active_site
IPR011009	Kinase-like_dom_sf	Homologous_superfamily
IPR017441	Protein_kinase_ATP_BS	Binding_site
IPR045216	CK2_alpha	Family

Pfam: PF00069

Catalyzed reactions (Rhea), 2 shown:

• L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) (RHEA:17989)
• L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+) (RHEA:46608)

UniProt features (13 total): sequence conflict 7, binding site 2, chain 1, domain 1, active site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEV1-F1	90.69	0.85

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 156 (proton acceptor)

Ligand- & substrate-binding residues (2): 45–53; 68

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9768727	Regulation of CDH1 posttranslational processing and trafficking to plasma membrane

MSigDB gene sets: 56 (showing top): GOBP_GROWTH, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CELL_GROWTH, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_DNA_DAMAGE_RESPONSE, GOBP_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_GROWTH, GOBP_PROTEIN_CATABOLIC_PROCESS, GOBP_CELL_GROWTH, GOCC_TRANSFERASE_COMPLEX_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOBP_REGULATION_OF_GROWTH

GO Biological Process (7): double-strand break repair (GO:0006302), protein phosphorylation (GO:0006468), positive regulation of cell population proliferation (GO:0008284), positive regulation of cell growth (GO:0030307), positive regulation of protein catabolic process (GO:0045732), regulation of cell cycle (GO:0051726), regulation of protein catabolic process (GO:0042176)

GO Molecular Function (8): protein serine/threonine kinase activity (GO:0004674), ATP binding (GO:0005524), protein serine kinase activity (GO:0106310), nucleotide binding (GO:0000166), protein kinase activity (GO:0004672), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), protein kinase CK2 complex (GO:0005956)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Regulation of CDH1 Expression and Function	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of cellular process	2
protein catabolic process	2
protein kinase activity	2
cellular anatomical structure	2
DNA repair	1
phosphorylation	1
protein modification process	1
cell population proliferation	1
regulation of cell population proliferation	1
regulation of cell growth	1
cell growth	1
positive regulation of growth	1
positive regulation of catabolic process	1
regulation of protein catabolic process	1
positive regulation of protein metabolic process	1
cell cycle	1
regulation of cellular process	1
regulation of catabolic process	1
regulation of protein metabolic process	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
kinase activity	1
phosphotransferase activity, alcohol group as acceptor	1
catalytic activity, acting on a protein	1
binding	1
transferase activity, transferring phosphorus-containing groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
intracellular protein-containing complex	1
serine/threonine protein kinase complex	1

Protein interactions and networks

STRING

1232 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSNK2A3	NOL6	Q9H6R4	551
CSNK2A3	MYLK	Q15746	404
CSNK2A3	CSNK2B	P07312	399
CSNK2A3	N0E472	N0E472	380
CSNK2A3	FLT4	P35916	372
CSNK2A3	KMT2E	Q8IZD2	353
CSNK2A3	BMPER	Q8N8U9	353
CSNK2A3	CDH5	P33151	350
CSNK2A3	EEF1E1	O43324	349
CSNK2A3	PSMA3	P25788	348
CSNK2A3	DDX17	Q92841	347
CSNK2A3	ADCK5	Q3MIX3	328
CSNK2A3	RPS6KC1	Q96S38	325
CSNK2A3	KDSR	Q06136	318
CSNK2A3	TP53	P04637	312

IntAct

27 interactions, top by confidence:

A	B	Type	Score
CSNK2B	NMT2	psi-mi:“MI:0914”(association)	0.660
SH3KBP1	USP27X	psi-mi:“MI:0914”(association)	0.640
CSNK2A2	PES1	psi-mi:“MI:0914”(association)	0.640
OSBPL8	CSNK2A2	psi-mi:“MI:0914”(association)	0.640
BHLHE23	CSNK2A2	psi-mi:“MI:0914”(association)	0.620
PRKCZ	IPO5	psi-mi:“MI:0914”(association)	0.530
GNL1	CSNK2A2	psi-mi:“MI:0914”(association)	0.530
HDGFL2	CDC7	psi-mi:“MI:0914”(association)	0.530
CFTR	CNOT1	psi-mi:“MI:0914”(association)	0.480
TCF7L2	LOC401309	psi-mi:“MI:0914”(association)	0.350
PRKCI	POLRMT	psi-mi:“MI:0914”(association)	0.350
RIPK1	TAF4	psi-mi:“MI:0914”(association)	0.350
SRC	ACTN4	psi-mi:“MI:0914”(association)	0.350
RPS6KA3	BAG2	psi-mi:“MI:0914”(association)	0.350
LYN	CDK1	psi-mi:“MI:0914”(association)	0.350
RIPK1	BAG2	psi-mi:“MI:0914”(association)	0.350
NOXO1	SOD1	psi-mi:“MI:0914”(association)	0.350
CSNK2B	OSBPL8	psi-mi:“MI:0914”(association)	0.350
CCNL1	AHCYL1	psi-mi:“MI:0914”(association)	0.350
GRAMD1B	MYCBP2	psi-mi:“MI:0914”(association)	0.350
HEXIM1	POLRMT	psi-mi:“MI:0914”(association)	0.350
HIRIP3	GPX1	psi-mi:“MI:0914”(association)	0.350
RNPS1	WWP2	psi-mi:“MI:0914”(association)	0.350
MAPT	DCTN6	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (113): CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-Western), CSNK2A3 (Affinity Capture-Western), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS), CSNK2A3 (Affinity Capture-MS)

ESM2 similar proteins: A2ZAB5, B6F107, O42099, O54833, O64812, O64816, O64817, O76484, P08181, P0C5D6, P18334, P19139, P19784, P20427, P21868, P21869, P28020, P28523, P28547, P33674, P40231, P43291, P43292, P45983, P49137, P49185, P68399, P68400, P79996, P92208, Q02720, Q08466, Q08467, Q3UMW7, Q4U925, Q5N942, Q60737, Q6ZI44, Q7XKA8, Q7XQP4

Diamond homologs: A0A194WDG1, A8WIP6, A8X5H5, B0Y4X4, B6F107, C4YGK0, G4N374, G4NH08, O04160, O08911, O13352, O23145, O42376, O54833, O61847, O64816, O64817, O76484, O94737, P00546, P08181, P14681, P15790, P18265, P18266, P18334, P19139, P19454, P19784, P20427, P21868, P21869, P23111, P24100, P28020, P28523, P28547, P29618, P29619, P33674

SIGNOR signaling

6 interactions.

A	Effect	B	Mechanism
CSNK2A3	“up-regulates activity”	FGF14	phosphorylation
CSNK2A3	“up-regulates activity”	SCN2A	phosphorylation
CSNK2A3	“down-regulates activity”	F8	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Platelet activation, signaling and aggregation	5	17.1×	1e-03
Signaling by Receptor Tyrosine Kinases	6	10.0×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

97 predictions. Top by Δscore:

Variant	Effect	Δscore
11:11351947:CTG:C	donor_gain	0.5800
11:11352393:CCAA:C	donor_gain	0.5800
11:11351946:A:AC	donor_gain	0.5300
11:11351947:C:CC	donor_gain	0.5300
11:11352452:G:A	donor_gain	0.5200
11:11352415:T:TA	donor_gain	0.5000
11:11352388:C:A	donor_gain	0.4400
11:11352548:CGG:C	donor_gain	0.4100
11:11352519:CAGG:C	donor_gain	0.4000
11:11352520:AGGA:A	donor_gain	0.4000
11:11352496:CAT:C	donor_gain	0.3900
11:11352522:G:GT	donor_gain	0.3900
11:11352386:ATC:A	donor_gain	0.3700
11:11352583:AG:A	donor_gain	0.3600
11:11352301:C:T	acceptor_gain	0.3500
11:11352462:A:AT	donor_gain	0.3500
11:11352518:TCAGG:T	donor_gain	0.3500
11:11352296:C:CC	acceptor_gain	0.3400
11:11352396:A:AC	donor_gain	0.3400
11:11352397:C:CC	donor_gain	0.3400
11:11352479:T:C	donor_gain	0.3400
11:11352584:G:C	donor_gain	0.3400
11:11352965:T:TA	donor_gain	0.3400
11:11352260:C:CC	acceptor_gain	0.3300
11:11352497:A:C	donor_gain	0.3300
11:11352516:G:C	donor_gain	0.3300
11:11352965:TC:T	donor_gain	0.3300
11:11352301:C:CT	acceptor_gain	0.3000
11:11352024:GTCC:G	acceptor_gain	0.2900
11:11352385:TATCC:T	donor_loss	0.2900

AlphaMissense

2566 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:11352594:A:G	W176R	0.998
11:11352594:A:T	W176R	0.998
11:11352785:A:T	V112D	0.997
11:11352599:A:T	I174K	0.994
11:11352577:A:C	F181L	0.993
11:11352577:A:T	F181L	0.993
11:11352579:A:G	F181L	0.993
11:11352958:A:C	F54L	0.993
11:11352958:A:T	F54L	0.993
11:11352960:A:G	F54L	0.993
11:11352605:C:G	R172P	0.991
11:11352679:A:C	C147W	0.991
11:11352857:A:C	L88W	0.991
11:11352866:A:G	L85S	0.991
11:11352917:T:A	K68I	0.990
11:11352866:A:C	L85W	0.989
11:11352916:T:A	K68N	0.989
11:11352916:T:G	K68N	0.989
11:11352954:C:G	A56P	0.989
11:11352967:A:C	S51R	0.989
11:11352967:A:T	S51R	0.989
11:11352969:T:G	S51R	0.989
11:11352602:A:G	L173P	0.988
11:11352168:C:G	A318P	0.987
11:11352857:A:G	L88S	0.987
11:11353050:A:G	W24R	0.987
11:11353050:A:T	W24R	0.987
11:11352593:C:G	W176S	0.986
11:11352680:C:T	C147Y	0.986
11:11352592:C:A	W176C	0.985

dbSNP variants (sampled 300 via entrez): RS1000624108 (11:11354263 G>A), RS1000655481 (11:11354624 G>A,C), RS1002060430 (11:11354648 A>G), RS1002346731 (11:11355174 A>G), RS1003416293 (11:11353413 T>C,G), RS1003750578 (11:11351453 C>T), RS1003851079 (11:11355232 A>G), RS1004863737 (11:11353831 G>A,C), RS1006524258 (11:11353808 A>G), RS1006870985 (11:11351818 C>G), RS1007308983 (11:11351985 G>A), RS1008545915 (11:11352814 T>C), RS1011482430 (11:11352013 G>A), RS1013277673 (11:11354684 T>C), RS1014739053 (11:11353358 A>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3832943 (PROTEIN FAMILY)

Molecules with ChEMBL bioactivity

11 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 315,707 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL58	MITOXANTRONE	4	166,878
CHEMBL3265032	ENTOSPLETINIB	3	1,628
CHEMBL50	QUERCETIN	3	74,559
CHEMBL105442	CI-1040	2	3,936
CHEMBL1230165	SILMITASERTIB	2	593
CHEMBL151	LUTEOLIN	2	23,523
CHEMBL1738758	ONVANSERTIB	2	780
CHEMBL31574	FISETIN	2	7,745
CHEMBL8260	BAICALEIN	2	8,592
CHEMBL83628	CHROMOCARB	2	1,533
CHEMBL150	KAEMPFEROL	1	25,940

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs7937567	Efficacy	3	cisplatin	Urinary Bladder Neoplasms

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs7937567	CSNK2A3, GALNT18	3	2.25	1	cisplatin

ChEMBL bioactivities

215 potent at pChembl≥5 of 223 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
10.08	Ki	0.084	nM	CHEMBL5419810
9.64	IC50	0.23	nM	CHEMBL4848224
9.42	Ki	0.38	nM	SILMITASERTIB
9.38	Ki	0.42	nM	CHEMBL4846181
9.38	Ki	0.42	nM	CHEMBL1682283
9.34	IC50	0.46	nM	CHEMBL4862003
9.22	IC50	0.6	nM	CHEMBL4872225
9.21	IC50	0.61	nM	CHEMBL4875513
9.18	IC50	0.66	nM	CHEMBL4860630
9.12	IC50	0.76	nM	CHEMBL4848072
9.10	IC50	0.79	nM	CHEMBL4875815
9.05	IC50	0.89	nM	CHEMBL4878998
8.81	IC50	1.54	nM	SILMITASERTIB
8.77	IC50	1.7	nM	CHEMBL4649511
8.75	IC50	1.78	nM	CHEMBL4857079
8.74	IC50	1.8	nM	SILMITASERTIB
8.64	IC50	2.3	nM	CHEMBL1682283
8.60	Ki	2.5	nM	CHEMBL5421618
8.52	IC50	3	nM	SILMITASERTIB
8.48	IC50	3.3	nM	CHEMBL5276409
8.46	IC50	3.5	nM	CHEMBL4637423
8.46	IC50	3.43	nM	CHEMBL4857107
8.34	IC50	4.53	nM	CHEMBL4867054
8.27	IC50	5.32	nM	CHEMBL4866502
8.25	IC50	5.66	nM	CHEMBL4855171
8.15	IC50	7	nM	CHEMBL4847656
8.14	IC50	7.29	nM	CHEMBL4849246
8.05	IC50	8.81	nM	CHEMBL4873444
8.05	IC50	9	nM	CHEMBL5421618
8.04	IC50	9.1	nM	CHEMBL1682297
8.03	IC50	9.33	nM	CHEMBL4854640
8.01	IC50	9.84	nM	CHEMBL4870899
7.95	IC50	11.34	nM	CHEMBL4870230
7.90	IC50	12.6	nM	CHEMBL4845902
7.89	Ki	13	nM	CHEMBL5414845
7.85	IC50	14	nM	CHEMBL4645915
7.84	IC50	14.28	nM	CHEMBL4846022
7.82	Ki	15	nM	CHEMBL5430283
7.77	IC50	16.82	nM	CHEMBL4865194
7.74	IC50	18.14	nM	CHEMBL4848229
7.72	IC50	19	nM	CHEMBL4637976
7.72	IC50	19	nM	CHEMBL501724
7.67	IC50	21.3	nM	CHEMBL4852239
7.67	IC50	21.65	nM	CHEMBL4850291
7.57	Ki	27	nM	CHEMBL3353413
7.50	IC50	32	nM	CHEMBL5430283
7.40	Ki	40	nM	CHEMBL376505
7.40	IC50	40	nM	CHEMBL5414845
7.40	IC50	40	nM	CHEMBL6151425
7.34	Ki	45.6	nM	CHEMBL6189175

PubChem BioAssay actives

203 with measured affinity, of 408 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(2S)-6-amino-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2R)-3-carboxy-2-[8-(4,5,6,7-tetraiodobenzimidazol-1-yl)octanoylamino]propanoyl]amino]propanoyl]amino]propanoyl]amino]propanoyl]amino]propanoyl]amino]propanoyl]amino]hexanoic acid	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0001	uM
2-fluoroethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0002	uM
5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	1750468: Inhibition of CK2 (unknown origin)	ki	0.0004	uM
5-(3-cyanoanilino)pyrimido[4,5-c]quinoline-8-carboxylic acid	1750468: Inhibition of CK2 (unknown origin)	ki	0.0004	uM
5-(3-ethynylanilino)pyrimido[4,5-c]quinoline-8-carboxylic acid	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0004	uM
5-(3-chloroanilino)-N-(2-morpholin-4-ylethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0005	uM
2,2-difluoroethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0006	uM
2-hydroxyethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0006	uM
5-(3-chloroanilino)-N-(2-hydroxyethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0007	uM
2-iodoethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0008	uM
methyl 3-[[5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carbonyl]amino]propanoate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0008	uM
N-(2-aminoethyl)-5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0009	uM
5-[[8-(hydroxyamino)-8-oxooctyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid;2,2,2-trifluoroacetic acid	1652189: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate preincubated for 30 mins followed by substrate addition and measured after 60 mins by ADP-Glo kinase assay	ic50	0.0017	uM
N-(2-bromoethyl)-5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0018	uM
4-(6,8-dibromo-3-hydroxy-4-oxochromen-2-yl)benzoic acid	2028061: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate incubated for 20 mins in presence of [gamma-32p]-ATP and ATP by beta-counter analysis	ki	0.0025	uM
(2Z)-7-bromo-2-[(3-bromo-4-hydroxyphenyl)methylidene]-1-benzofuran-3-one	1934407: Inhibition of recombinant human CK2 using RRRDDDSDDD as substrate in presence of [gamma-33P-ATP] incubated for 20 mins by beta-counter analysis	ic50	0.0033	uM
3,3-dichloropropyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0034	uM
5-[[6-(hydroxyamino)-6-oxohexyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid;2,2,2-trifluoroacetic acid	1652189: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate preincubated for 30 mins followed by substrate addition and measured after 60 mins by ADP-Glo kinase assay	ic50	0.0035	uM
methyl 4-[[5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carbonyl]amino]butanoate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0045	uM
N-(3-aminopropyl)-5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0053	uM
5-(3-chloroanilino)-N-hydroxybenzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0057	uM
5-bromo-2-methoxy-4-[(E)-(3-methylsulfanyl-5-phenyl-1,2,4-triazol-4-yl)iminomethyl]phenol	2028069: Inhibition of CK2 (unknown origin) incubated for 1.5 hrs in presence of ATP by kinase-glo luminescent kinase assay	ic50	0.0070	uM
2-pyridin-2-ylethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0073	uM
5-(3-chloroanilino)-N-(3-hydroxypropyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0088	uM
3-(cyclopropylamino)-5-[3-(trifluoromethyl)anilino]pyrimido[4,5-c]quinoline-8-carboxylic acid	2028058: Inhibition of CK2 (unknown origin)	ic50	0.0091	uM
5-(3-chloroanilino)-N-methylsulfonylbenzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0093	uM
3-[[5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carbonyl]amino]propanoic acid	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0098	uM
2-[2-(2-hydroxyethoxy)ethoxy]ethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0113	uM
5-(3-chloroanilino)-N-(2-piperidin-1-ylethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0126	uM
4-(6,8-dichloro-3-hydroxy-4-oxochromen-2-yl)benzoic acid	2028061: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate incubated for 20 mins in presence of [gamma-32p]-ATP and ATP by beta-counter analysis	ki	0.0130	uM
5-[[7-(hydroxyamino)-7-oxoheptyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid;2,2,2-trifluoroacetic acid	1652189: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate preincubated for 30 mins followed by substrate addition and measured after 60 mins by ADP-Glo kinase assay	ic50	0.0140	uM
5-(3-chloroanilino)-N-(2,2-difluoroethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0143	uM
2-(hydroxymethyl)-5-(4,5,6,7-tetrabromobenzimidazol-1-yl)oxolan-3-ol	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0150	uM
5-(3-chloroanilino)-N-(2-pyrrolidin-1-ylethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0168	uM
5-(3-chloroanilino)-N-prop-2-ynylbenzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0181	uM
5-[[9-(hydroxyamino)-9-oxononyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid;2,2,2-trifluoroacetic acid	1652189: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate preincubated for 30 mins followed by substrate addition and measured after 60 mins by ADP-Glo kinase assay	ic50	0.0190	uM
5-(3-chloroanilino)-N-[2-(dimethylamino)ethyl]benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0213	uM
4-[[5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carbonyl]amino]butanoic acid	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0216	uM
7-methyl-5-propan-2-yl-7,8-dihydro-6H-indeno[1,2-b]indole-9,10-dione	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0270	uM
4,5,6,7-tetrabromo-N,N-dimethyl-1H-benzimidazol-2-amine	1750468: Inhibition of CK2 (unknown origin)	ki	0.0400	uM
(2Z)-6-[(2,6-dichlorophenyl)sulfonylmethyl]-2-[(4-hydroxy-3-nitrophenyl)methylidene]-4H-1,4-benzothiazin-3-one	2028058: Inhibition of CK2 (unknown origin)	ic50	0.0500	uM
1,2,5,8-tetrahydroxyanthracene-9,10-dione	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0600	uM
7,18-dioxapentacyclo[11.7.0.03,11.04,8.015,19]icosa-1(20),2,4(8),5,9,11,13,15(19),16-nonaene-6,16-dicarboxylic acid	2028058: Inhibition of CK2 (unknown origin)	ic50	0.0630	uM
N-(5-methoxy-1,3-benzothiazol-2-yl)-4-oxochromene-2-carboxamide	1873357: Inhibition of CK2 (unknown origin)	ic50	0.0800	uM
[1]benzofuro[6,5-e][1]benzofuran-2,8-dicarboxylic acid	2028058: Inhibition of CK2 (unknown origin)	ic50	0.1000	uM
2-(2-chloro-4-iodoanilino)-N-(cyclopropylmethoxy)-3,4-difluorobenzamide	1614769: Inhibition of CK2 in human 786-0 cells assessed as decrease in Akt1 phosphorylation at Ser129 after 24 hrs by Western blot analysis	ec50	0.1000	uM
N-(5-fluoro-1,3-benzothiazol-2-yl)-4-oxochromene-2-carboxamide	1873357: Inhibition of CK2 (unknown origin)	ic50	0.1100	uM
(2Z,5Z)-5-(1,3-benzodioxol-5-ylmethylidene)-2-pyridin-2-yliminoimidazolidin-4-one	1871894: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate incubated for 30 mins in presence of ATP by scintillation counting method	ic50	0.1300	uM
(4Z)-4-(1,3-benzodioxol-5-ylmethylidene)-2-(4-hydroxyanilino)-1H-imidazol-5-one	1871894: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate incubated for 30 mins in presence of ATP by scintillation counting method	ic50	0.1400	uM
N-[4-(4-fluorophenyl)-1,3-thiazol-2-yl]-4-oxochromene-2-carboxamide	1873357: Inhibition of CK2 (unknown origin)	ic50	0.1500	uM

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
lead acetate	decreases expression	1
nickel sulfate	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Temozolomide	increases expression	1
Cisplatin	increases expression	1
Quercetin	affects binding	1
Lactic Acid	affects expression	1

ChEMBL screening assays

153 unique, capped per target: 153 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1024750	Binding	Inhibition of human recombinant casein kinase 2 subunit alpha2beta2 expressed in Escherichia coli BL21 (DE3) assessed as [32P] incorporation by liquid scintillation counting	Synthesis of new analogs of benzotriazole, benzimidazole and phthalimide–potential inhibitors of human protein kinase CK2. — Bioorg Med Chem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D7N2	Ubigene A-549 CSNK2A3 KO	Cancer cell line	Male
CVCL_D8JJ	Ubigene HCT 116 CSNK2A3 KO	Cancer cell line	Male
CVCL_E0B9	Ubigene HeLa CSNK2A3 KO	Cancer cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.