CDK3

Summary

CDK3 (cyclin dependent kinase 3, HGNC:1772) is a protein-coding gene on chromosome 17q25.1, encoding Cyclin-dependent kinase 3 (Q00526). Serine/threonine-protein kinase that plays a critical role in the control of the eukaryotic cell cycle; involved in G0-G1 and G1-S cell cycle transitions.

This gene encodes a member of the cyclin-dependent protein kinase family. The protein promotes entry into S phase, in part by activating members of the E2F family of transcription factors. The protein also associates with cyclin C and phosphorylates the retinoblastoma 1 protein to promote exit from G0.

Source: NCBI Gene 1018 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 35 total
• Druggable target: yes — 29 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_001258

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1772
Approved symbol	CDK3
Name	cyclin dependent kinase 3
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000250506
Ensembl biotype	protein_coding
OMIM	123828
Entrez	1018

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000425876, ENST00000448471, ENST00000586261, ENST00000864464, ENST00000935236

RefSeq mRNA: 1 — MANE Select: NM_001258 NM_001258

CCDS: CCDS11736

Canonical transcript exons

ENST00000448471 — 8 exons

Exon	Start	End
ENSE00003801733	76002248	76002418
ENSE00003802883	76001874	76001951
ENSE00003803615	76002022	76002142
ENSE00003804070	76003195	76003398
ENSE00003804419	76002511	76002612
ENSE00003805282	76001412	76001541
ENSE00003809568	76000855	76000967
ENSE00003931175	76005298	76005998

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 91.96.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	91.96	gold quality
right lobe of liver	UBERON:0001114	89.64	gold quality
lower esophagus mucosa	UBERON:0035834	87.63	gold quality
granulocyte	CL:0000094	86.96	gold quality
pituitary gland	UBERON:0000007	86.77	gold quality
right lobe of thyroid gland	UBERON:0001119	86.76	gold quality
right uterine tube	UBERON:0001302	86.18	gold quality
adenohypophysis	UBERON:0002196	86.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.93	gold quality
prostate gland	UBERON:0002367	85.89	gold quality
spleen	UBERON:0002106	85.72	gold quality
left lobe of thyroid gland	UBERON:0001120	85.68	gold quality
thyroid gland	UBERON:0002046	85.30	gold quality
skin of abdomen	UBERON:0001416	84.96	gold quality
transverse colon	UBERON:0001157	84.72	gold quality
zone of skin	UBERON:0000014	84.01	gold quality
endocervix	UBERON:0000458	83.88	gold quality
right ovary	UBERON:0002118	83.77	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.72	gold quality
skin of leg	UBERON:0001511	83.57	gold quality
left ovary	UBERON:0002119	83.30	gold quality
minor salivary gland	UBERON:0001830	83.14	gold quality
body of uterus	UBERON:0009853	82.96	gold quality
metanephros cortex	UBERON:0010533	82.89	gold quality
upper lobe of left lung	UBERON:0008952	82.74	gold quality
vagina	UBERON:0000996	82.64	gold quality
saliva-secreting gland	UBERON:0001044	82.60	gold quality
body of stomach	UBERON:0001161	82.45	gold quality
omental fat pad	UBERON:0010414	82.44	gold quality
small intestine	UBERON:0002108	82.31	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.72

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF1, MYCN

miRNA regulators (miRDB)

9 targeting CDK3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3199	99.17	65.19	696
HSA-MIR-8052	99.17	65.01	719
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-6755-3P	98.61	66.90	834
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-4723-3P	97.67	65.91	1017
HSA-MIR-6769B-3P	97.41	65.53	1036
HSA-MIR-3183	97.40	65.68	978
HSA-MIR-125A-3P	97.04	66.92	902

Literature-anchored findings (GeneRIF, showing 13)

• A non-cdk8-associated cellular pool of cyclin C combines with cdk3 to stimulate pRb phosphorylation at S807/811 during the G0/G1 transition, and this phosphorylation is required for cells to exit G0 efficiently. (PMID:15084261)
• Expression level of cdk3 is higher in human cancer cell lines and glioblastoma tissue compared with normal brain tissue. cdk3 phosphorylates activating transcription factor 1 (ATF1)and enhances the transactivation and transcriptional activities of ATF1. (PMID:18794154)
• The Walleye dermal sarcoma virus cyclin functions as a structural ortholog of cyclin C in spite of its limited amino acid sequence identity with C cyclins or with any known cyclins and activates Cdk8 and Cdk3. (PMID:21067790)
• CDK3 is associated with the progression of NPC, and may be a potential biomarker for prediction of the prognosis of patients with NPC. (PMID:24691537)
• Mir-873 inhibits ESR1 activity and cell growth via targeting CDK3. (PMID:25531331)
• Data indicate that microRNA miR-214 has tumor-suppressive activity in hepatocellular carcinoma (HCC) through inhibition of E2F2 transcription factor (E2F2), cyclin-dependent kinases CDK3 and CDK6. (PMID:26498144)
• High Cdk3-promoted epithelial-mesenchymal transition through activating AP-1 is involved in colorectal cancer metastasis. (PMID:26755651)
• These results provided evidence supporting the oncogenic potential of NFAT3 and suggested that CDK3-mediated phosphorylation of NFAT3 has an important role in skin tumorigenesis. (PMID:27893713)
• The analysis of tumor and matched normal lung tissues indicates that miR-150 downregulation in lung tumors correlates with higher CDK3 levels. In addition, miR-150 transfection experiments with cancer-derived cell lines reveal that miR-150-mediated CDK3 suppression directly induces growth inhibition. (PMID:28108217)
• ectopic expression of HuR promotes breast cancer cell proliferation and survival by directly binding to and stabilizing CDK3 mRNA. (PMID:28501005)
• These results suggest that miR-125a-3p can function as a novel tumor suppressor in ER(+) breast cancer by targeting CDK3, which may be a potential therapeutic approach for TamR breast cancer therapy (PMID:28939591)
• HuR facilitated lung cancer stemness dependent on CDK3 expression. miR-873 or miR-125a-3p level was negatively correlated with HuR and CDK3 expression levels in lung cancer tissues. HuR facilitates lung cancer stemness via regulating miR-873/CDK3 and miR-125a-3p/CDK3 axis. (PMID:29344850)
• circRNA_141539 can serve as an oncogenic factor in esophageal squamous cell carcinoma by sponging miR-4469 and activating CDK3 gene. (PMID:33504681)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cdk3	ENSMUSG00000092300
drosophila_melanogaster	Cdk2	FBGN0004107

Paralogs (26): CDKL3 (ENSG00000006837), CDKL5 (ENSG00000008086), CDK11A (ENSG00000008128), CDK14 (ENSG00000058091), CDK17 (ENSG00000059758), CDK13 (ENSG00000065883), CDKL1 (ENSG00000100490), CDK16 (ENSG00000102225), CDK6 (ENSG00000105810), PRP4K (ENSG00000112739), CDK18 (ENSG00000117266), CDK2 (ENSG00000123374), CDK8 (ENSG00000132964), CDK7 (ENSG00000134058), CDK4 (ENSG00000135446), CDK9 (ENSG00000136807), CDK15 (ENSG00000138395), CDKL2 (ENSG00000138769), CDK19 (ENSG00000155111), CDK20 (ENSG00000156345), CDK5 (ENSG00000164885), CDK12 (ENSG00000167258), CDK1 (ENSG00000170312), CDK10 (ENSG00000185324), CDKL4 (ENSG00000205111), CDK11B (ENSG00000248333)

Protein

Protein identifiers

Cyclin-dependent kinase 3 — Q00526 (reviewed: Q00526)

Alternative names: Cell division protein kinase 3

All UniProt accessions (2): Q00526, K7EJ83

UniProt curated annotations — full annotation on UniProt →

Function. Serine/threonine-protein kinase that plays a critical role in the control of the eukaryotic cell cycle; involved in G0-G1 and G1-S cell cycle transitions. Interacts with CCNC/cyclin-C during interphase. Phosphorylates histone H1, ATF1, RB1 and CABLES1. ATF1 phosphorylation triggers ATF1 transactivation and transcriptional activities, and promotes cell proliferation and transformation. CDK3/cyclin-C mediated RB1 phosphorylation is required for G0-G1 transition. Promotes G1-S transition probably by contributing to the activation of E2F1, E2F2 and E2F3 in a RB1-independent manner.

Subunit / interactions. Interacts with CABLES1 and CABLES2. Interacts with ATF1. Binding to CCNC/cyclin-C promotes RB1 phosphorylation.

Tissue specificity. Expressed in cancer cell lines and glioblastoma tissue.

Similarity. Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.

RefSeq proteins (1): NP_001249* (*=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
IPR050108	CDK	Family

Pfam: PF00069

Enzyme classification (BRENDA):

• EC 2.7.11.22 — cyclin-dependent kinase (BRENDA: 49 organisms, 441 substrates, 555 inhibitors, 8 Km, 4 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ADAQHATPPKKKRKVEDPKDF	0.046–0.521	2
ATP	0.0052–0.017	2
FIN1	0.003	1
PKTPKKAKKL	0.0029	1

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 (38 total): helix 15, strand 9, sequence variant 5, turn 4, binding site 2, chain 1, domain 1, active site 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7XQK	X-RAY DIFFRACTION	2.25
8H4R	X-RAY DIFFRACTION	2.75

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q00526-F1	86.31	0.61

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): 127 (proton acceptor)

Ligand- & substrate-binding residues (2): 10–18; 33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 75 (showing top): WANG_CLIM2_TARGETS_UP, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_NEGATIVE_REGULATION_OF_NOTCH_SIGNALING_PATHWAY, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_DNA_DAMAGE_RESPONSE, GOBP_MITOTIC_CELL_CYCLE, GOBP_REGULATION_OF_NOTCH_SIGNALING_PATHWAY, GOBP_CELL_CYCLE_G2_M_PHASE_TRANSITION, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, MODULE_124, GOCC_TRANSFERASE_COMPLEX_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GOCC_TRANSFERASE_COMPLEX, GOCC_PROTEIN_KINASE_COMPLEX

GO Biological Process (10): G1/S transition of mitotic cell cycle (GO:0000082), DNA damage response (GO:0006974), signal transduction (GO:0007165), cell population proliferation (GO:0008283), regulation of G2/M transition of mitotic cell cycle (GO:0010389), regulation of gene expression (GO:0010468), G0 to G1 transition (GO:0045023), negative regulation of Notch signaling pathway (GO:0045746), cell division (GO:0051301), protein phosphorylation (GO:0006468)

GO Molecular Function (10): cyclin-dependent protein serine/threonine kinase activity (GO:0004693), ATP binding (GO:0005524), cyclin binding (GO:0030332), protein serine kinase activity (GO:0106310), nucleotide binding (GO:0000166), protein kinase activity (GO:0004672), protein serine/threonine kinase activity (GO:0004674), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (3): cyclin-dependent protein kinase holoenzyme complex (GO:0000307), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	3
protein kinase activity	2
mitotic cell cycle	1
mitotic cell cycle phase transition	1
cell cycle G1/S phase transition	1
cellular response to stress	1
cell communication	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
G2/M transition of mitotic cell cycle	1
regulation of mitotic cell cycle phase transition	1
regulation of cell cycle G2/M phase transition	1
gene expression	1
regulation of macromolecule biosynthetic process	1
cell cycle process	1
Notch signaling pathway	1
regulation of Notch signaling pathway	1
negative regulation of signal transduction	1
phosphorylation	1
protein modification process	1
protein serine/threonine kinase activity	1
cyclin-dependent protein kinase activity	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
protein 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
serine/threonine protein kinase complex	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2981 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDK3	CCNC	P24863	995
CDK3	CABLES1	Q8TDN4	945
CDK3	CCNL2	Q96S94	903
CDK3	CDK4	P11802	771
CDK3	CCNA1	P78396	762
CDK3	CDK2	P24941	703
CDK3	CCNH	P51946	691
CDK3	CCNE2	O96020	652
CDK3	CDKN2A	P42771	598
CDK3	CCNB1	P14635	587
CDK3	CCND1	P24385	586
CDK3	CCNA2	P20248	585
CDK3	CDKN1A	P38936	582
CDK3	CDCA8	Q53HL2	548
CDK3	CDC37	Q16543	546

IntAct

124 interactions, top by confidence:

A	B	Type	Score
CCNC	CDK8	psi-mi:“MI:0914”(association)	0.980
CDK2	CCNE2	psi-mi:“MI:0914”(association)	0.940
CDK2	CCNB2	psi-mi:“MI:0914”(association)	0.860
CDKN1A	CDK3	psi-mi:“MI:0915”(physical association)	0.850
CDK5	FIBP	psi-mi:“MI:0914”(association)	0.840
CDK1	CCNB2	psi-mi:“MI:0914”(association)	0.840
CKS1B	CDK3	psi-mi:“MI:0915”(physical association)	0.800
CCNC	CDK3	psi-mi:“MI:0915”(physical association)	0.750
CKS2	CDK3	psi-mi:“MI:0915”(physical association)	0.740
STK4	MAP1B	psi-mi:“MI:0914”(association)	0.730
HSP90AB1	CDK3	psi-mi:“MI:0915”(physical association)	0.670
CCNE2	CDK3	psi-mi:“MI:0915”(physical association)	0.660
CDK2	GMNN	psi-mi:“MI:0914”(association)	0.640
CDK3	CCNA2	psi-mi:“MI:0914”(association)	0.640
CDK3	CCNH	psi-mi:“MI:0915”(physical association)	0.560
CDK3	CCNI	psi-mi:“MI:0915”(physical association)	0.560
CDK3	LHX4	psi-mi:“MI:0915”(physical association)	0.560
PAX6	CDK3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (172): CDK3 (Affinity Capture-MS), CDK3 (Affinity Capture-MS), CDK3 (Affinity Capture-MS), CDK3 (Affinity Capture-MS), CDK3 (Affinity Capture-MS), HSP90AA1 (Affinity Capture-MS), HSP90AB1 (Affinity Capture-MS), HSP90AB4P (Affinity Capture-MS), HSP90AA5P (Affinity Capture-MS), HSPA1L (Affinity Capture-MS), CDT1 (Affinity Capture-MS), FKBP5 (Affinity Capture-MS), GMNN (Affinity Capture-MS), CCNE1 (Affinity Capture-MS), CCNE2 (Affinity Capture-MS)

ESM2 similar proteins: O55076, O74456, O96821, P06493, P11440, P13863, P23111, P23437, P24033, P24100, P24923, P24941, P29618, P29619, P34112, P34117, P35567, P39951, P43450, P48609, P48734, P48963, P49615, P51166, P51958, P52389, P93101, Q00526, Q00535, Q02399, Q03114, Q05006, Q07785, Q26671, Q27032, Q2PQN9, Q38772, Q38773, Q41639, Q4Y4B1

Diamond homologs: A1CL96, A1D624, A2QU77, A2X6X1, A2XUW1, A3LUB9, A4QXX4, A8XA58, O13958, O55076, O61847, O96821, P00546, P06493, P0C661, P0CS76, P0CS77, P11440, P21127, P23111, P23437, P23572, P24033, P24100, P24788, P24923, P24941, P29618, P29619, P34112, P34117, P34556, P35567, P39073, P39951, P43063, P43450, P46892, P48734, P48963

SIGNOR signaling

19 interactions.

A	Effect	B	Mechanism
CDK3	down-regulates	RB1	phosphorylation
CDK3	up-regulates	ATF1	phosphorylation
CDK3	up-regulates	JUN	phosphorylation
CDK3	down-regulates	TFCP2	phosphorylation
4-(2,6-dichlorobenzamido)-N-(piperidin-4-yl)-pyrazole-3-carboxamide	down-regulates	CDK3	“chemical inhibition”
CDK3	up-regulates	LIN9	phosphorylation
CDK3	“form complex”	CyclinC/CDK3	binding
CDK3	“up-regulates activity”	NFATC4	phosphorylation
CDKN1A	down-regulates	CDK3	binding
CDK3	unknown	CABLES1	phosphorylation
CDK3	“down-regulates quantity by destabilization”	NOTCH1	phosphorylation
CDK3	“form complex”	CyclinE1/CDK3	binding
CDK3	“up-regulates activity”	ESR1	phosphorylation
CDK3	“up-regulates activity”	MECOM	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 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
TP53 Regulates Transcription of Cell Cycle Genes	6	68.0×	3e-08
G1 Phase	5	41.0×	5e-06
Cyclin D associated events in G1	7	34.0×	1e-07
Cyclin A/B1/B2 associated events during G2/M transition	5	32.1×	1e-05
SCF(Skp2)-mediated degradation of p27/p21	7	30.3×	2e-07
Cyclin E associated events during G1/S transition	5	29.7×	1e-05
G1/S Transition	6	29.1×	3e-06
Cyclin A:Cdk2-associated events at S phase entry	5	27.7×	2e-05

GO biological processes:

GO term	Partners	Fold	FDR
G1/S transition of mitotic cell cycle	11	35.0×	8e-12
regulation of mitotic cell cycle	5	19.1×	1e-03
animal organ morphogenesis	5	15.2×	2e-03
cell division	11	8.1×	3e-05
regulation of cell cycle	6	7.1×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1259 predictions. Top by Δscore:

Variant	Effect	Δscore
17:76001537:GATTT:G	donor_gain	1.0000
17:76001542:G:GG	donor_gain	1.0000
17:76001872:AG:A	acceptor_gain	1.0000
17:76001873:GG:G	acceptor_gain	1.0000
17:76001947:GTCCG:G	donor_gain	1.0000
17:76001949:CCGG:C	donor_loss	1.0000
17:76001949:CCGGT:C	donor_loss	1.0000
17:76001950:CGGT:C	donor_loss	1.0000
17:76001950:CGGTG:C	donor_loss	1.0000
17:76001952:G:A	donor_loss	1.0000
17:76001952:G:GG	donor_gain	1.0000
17:76001953:T:G	donor_loss	1.0000
17:76001953:TGA:T	donor_loss	1.0000
17:76001954:GA:G	donor_loss	1.0000
17:76001954:GAG:G	donor_loss	1.0000
17:76002018:TCA:T	acceptor_loss	1.0000
17:76002019:CAGA:C	acceptor_loss	1.0000
17:76002020:A:AC	acceptor_loss	1.0000
17:76002020:A:AG	acceptor_gain	1.0000
17:76002020:A:G	acceptor_loss	1.0000
17:76002020:AGACT:A	acceptor_gain	1.0000
17:76002021:G:GA	acceptor_gain	1.0000
17:76002021:GA:G	acceptor_gain	1.0000
17:76002021:GAC:G	acceptor_gain	1.0000
17:76002021:GACT:G	acceptor_gain	1.0000
17:76002021:GACTG:G	acceptor_gain	1.0000
17:76002091:G:GT	donor_gain	1.0000
17:76002114:GC:G	donor_gain	1.0000
17:76002139:CAAGG:C	donor_loss	1.0000
17:76002140:AAG:A	donor_loss	1.0000

AlphaMissense

1984 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:76001524:G:C	K33N	1.000
17:76001524:G:T	K33N	1.000
17:76002309:G:C	R126P	1.000
17:76002312:A:C	D127A	1.000
17:76002312:A:G	D127G	1.000
17:76002312:A:T	D127V	1.000
17:76002365:G:C	D145H	1.000
17:76002366:A:T	D145V	1.000
17:76002367:C:A	D145E	1.000
17:76002367:C:G	D145E	1.000
17:76001462:G:C	G13R	0.999
17:76001462:G:T	G13C	0.999
17:76001472:G:A	G16E	0.999
17:76001517:C:A	A31D	0.999
17:76001520:T:C	L32P	0.999
17:76001906:G:T	R50M	0.999
17:76002311:G:C	D127H	0.999
17:76002313:C:A	D127E	0.999
17:76002313:C:G	D127E	0.999
17:76002315:T:C	L128P	0.999
17:76002319:G:C	K129N	0.999
17:76002319:G:T	K129N	0.999
17:76002326:A:G	N132D	0.999
17:76002328:C:A	N132K	0.999
17:76002328:C:G	N132K	0.999
17:76002330:T:C	L133P	0.999
17:76002366:A:C	D145A	0.999
17:76002366:A:G	D145G	0.999
17:76002375:T:C	L148P	0.999
17:76002518:C:T	T165I	0.999

dbSNP variants (sampled 300 via entrez): RS1000606997 (17:76000518 C>A,T), RS1001185304 (17:76001695 G>A), RS1001427164 (17:76002031 C>T), RS1001956787 (17:76006054 T>C), RS1002475516 (17:76000398 T>C), RS1002590245 (17:76000489 G>A), RS1002961795 (17:76004768 C>T), RS1005064780 (17:75999988 T>C,G), RS1005464726 (17:76004865 G>A), RS1005565373 (17:76002721 G>A,C), RS1005586998 (17:76006278 G>A), RS1005826277 (17:76003054 T>C), RS1006741704 (17:76003817 A>G), RS1007422043 (17:76002180 C>T), RS1008017613 (17:76000745 G>C)

Disease associations

OMIM: gene MIM:123828 | 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 (6): CHEMBL2111444 (PROTEIN COMPLEX GROUP), CHEMBL3038471 (PROTEIN COMPLEX), CHEMBL3559691 (PROTEIN FAMILY), CHEMBL4442 (SINGLE PROTEIN), CHEMBL4523635 (PROTEIN COMPLEX), CHEMBL4888443 (PROTEIN COMPLEX)

Molecules with ChEMBL bioactivity

29 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 224,008 (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
CHEMBL1336	SORAFENIB	4	86,060
CHEMBL502835	NINTEDANIB	4	8,545
CHEMBL535	SUNITINIB	4	79,020
CHEMBL2105728	CRENOLANIB	3	2,167
CHEMBL300138	ENZASTAURIN	3	3,209
CHEMBL428690	ALVOCIDIB	3	27,781
CHEMBL522892	DOVITINIB	3	4,944
CHEMBL603469	LESTAURTINIB	3
CHEMBL1944698	ZOTIRACICLIB	2	2,915
CHEMBL4442620	RONICICLIB	2	367
CHEMBL445813	AT-7519	2	2,614
CHEMBL5199065	ISTISOCICLIB	2	21
CHEMBL1276127	INDIRUBIN	2	181
CHEMBL1231124	AZD-1480	2	1,576
CHEMBL1738757	REBASTINIB	2	1,478
CHEMBL384304	RG-547	2	93
CHEMBL402548	DANUSERTIB	2	1,928
CHEMBL4462530	ZEMIRCICLIB	2	429
CHEMBL4439321	ATUVECICLIB	1	129
CHEMBL3545083	RGB-286638	1	551
CHEMBL5834528	INX-315	1
CHEMBL1084546	PF-00562271	1
CHEMBL1230607	PHA-793887	1
CHEMBL2041933	AZD-7762	1
CHEMBL296468	BMS-387032	1
CHEMBL3128043	PF-03758309	1
CHEMBL3545085	XL-228	1
CHEMBL4289017	PF-03814735	1
CHEMBL574738	AST-487	1

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — CDK1 subfamily

Most potent curated ligand interactions (2 total), top 2:

Ligand	Action	Affinity	Parameter
RGB-286638	Inhibition	8.3	pIC50
zotiraciclib	Inhibition	8.1	pIC50

Binding affinities (BindingDB)

9 measured of 9 human assays (9 total across all organisms); most potent 9 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
Staurosporine	KD	1.7 nM
3-[2-(cyclopropanecarbonylamino)-[1,3]thiazolo[5,4-b]pyridin-5-yl]-N-[4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]benzamide	KD	57 nM	US-8765747: Fused 2-aminothiazole compounds
Pyrazolopyrimidone analog, RGB-286147	IC50	71 nM
cis-(1S,3R)-3-acetamido-N-[4-(4-fluoro-2-methoxyphenyl)-2-pyridinyl]cyclohexane-1-carboxamide	IC50	94 nM	US-9067888: Inhibitors of protein kinases
1-[4-[(4-ethyl-1-piperazinyl)methyl]-3-(trifluoromethyl)phenyl]-3-[4-[[6-(methylamino)-4-pyrimidinyl]oxy]phenyl]urea	KD	1400 nM
BMS-387072	KD	1800 nM
3-acetamido-N-[4-(4-fluoro-2-methoxyphenyl)-2-pyridinyl]cyclopentane-1-carboxamide	IC50	1880 nM	US-9067888: Inhibitors of protein kinases
1-Acyl-1H-[1,2,4]triazole-3,5-diamine Analogue 3b	KD	3100 nM
2-(2-chlorophenyl)-5,7-dihydroxy-8-[(3S)-3-hydroxy-1-methyl-4-piperidinyl]-1-benzopyran-4-one	KD	5300 nM

ChEMBL bioactivities

204 potent at pChembl≥5 of 209 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
9.22	IC50	0.6	nM	CHEMBL3716786
9.10	IC50	0.8	nM	RG-547
9.03	IC50	0.94	nM	CHEMBL5808524
8.77	IC50	1.69	nM	STAUROSPORINE
8.70	IC50	2	nM	RGB-286638
8.68	IC50	2.08	nM	STAUROSPORINE
8.55	IC50	2.8	nM	CHEMBL5837976
8.54	IC50	2.89	nM	STAUROSPORINE
8.52	IC50	3	nM	ZOTIRACICLIB
8.51	IC50	3.1	nM	STAUROSPORINE
8.49	Kd	3.2	nM	RG-547
8.40	IC50	4	nM	STAUROSPORINE
8.30	IC50	5	nM	RONICICLIB
8.30	IC50	5	nM	CHEMBL5747791
8.23	IC50	5.9	nM	CHEMBL3717691
8.22	IC50	6	nM	CHEMBL5776705
8.22	IC50	6	nM	CHEMBL5739950
8.16	IC50	6.9	nM	STAUROSPORINE
8.10	Kd	8	nM	PHA-793887
8.10	IC50	8	nM	ZOTIRACICLIB
8.10	IC50	8	nM	CHEMBL5992870
8.06	IC50	8.7	nM	CHEMBL3717995
8.05	IC50	9	nM	RONICICLIB
8.00	IC50	9.9	nM	INX-315
8.00	IC50	10	nM	CHEMBL5938366
8.00	IC50	10	nM	CHEMBL5945627
7.95	IC50	11.2	nM	CHEMBL4848734
7.92	IC50	12	nM	CHEMBL3718389
7.92	IC50	12	nM	CHEMBL3719311
7.89	IC50	13	nM	CHEMBL5943225
7.80	IC50	16	nM	CHEMBL3719096
7.75	IC50	18	nM	CHEMBL5797283
7.70	IC50	20	nM	CHEMBL4754081
7.68	IC50	21	nM	CHEMBL3716783
7.66	IC50	22	nM	CHEMBL3719241
7.64	IC50	23	nM	CHEMBL3717041
7.64	IC50	23	nM	CHEMBL3719041
7.64	IC50	23	nM	ZEMIRCICLIB
7.64	IC50	23	nM	CHEMBL6021151
7.64	IC50	23	nM	CHEMBL5980280
7.55	IC50	28	nM	CHEMBL3716298
7.55	IC50	28	nM	CHEMBL5778396
7.54	IC50	29	nM	CHEMBL3716137
7.54	IC50	29	nM	CHEMBL4579344
7.54	IC50	29	nM	CHEMBL5932925
7.52	IC50	30	nM	CHEMBL3715917
7.52	Kd	30	nM	STAUROSPORINE
7.50	Kd	32	nM	K-252A
7.48	IC50	33	nM	CHEMBL3718495
7.47	IC50	34	nM	CHEMBL5845618

PubChem BioAssay actives

89 with measured affinity, of 1045 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
[4-amino-2-[(1-methylsulfonylpiperidin-4-yl)amino]pyrimidin-5-yl]-(2,3-difluoro-6-methoxyphenyl)methanone	1890133: Inhibition of CDK3 (unknown origin) by kinase selectivity assay	ic50	0.0008	uM
(2S,3R,4R,6R)-3-methoxy-2-methyl-4-(methylamino)-29-oxa-1,7,17-triazaoctacyclo[12.12.2.12,6.07,28.08,13.015,19.020,27.021,26]nonacosa-8,10,12,14,19,21,23,25,27-nonaen-16-one	1715410: Inhibition of human CDK3/cyclin-E using histone H1 as substrate by [gamma-33P]-ATP assay	ic50	0.0017	uM
1-[3-[4-[[4-(2-methoxyethyl)piperazin-1-yl]methyl]phenyl]-4-oxo-1H-indeno[2,1-d]pyrazol-5-yl]-3-morpholin-4-ylurea	1317362: Inhibition of CDK3/cyclin E (unknown origin)	ic50	0.0020	uM
(16E)-14-methyl-20-oxa-5,7,14,27-tetrazatetracyclo[19.3.1.12,6.18,12]heptacosa-1(25),2(27),3,5,8,10,12(26),16,21,23-decaene	1317352: Inhibition of recombinant human full length C-terminal His6-tagged CDK3/N-terminal GST-tagged cyclin E expressed in baculovirus infected Sf21 insect cells using Histone H1 as substrate	ic50	0.0030	uM
(2R,3R)-3-[2-[4-(cyclopropylsulfonimidoyl)anilino]-5-(trifluoromethyl)pyrimidin-4-yl]oxybutan-2-ol	1845582: Inhibition of CDK3 (unknown origin) expressed in baculovirus-infected Sf9 insect cells	ic50	0.0050	uM
N-[6,6-dimethyl-5-(1-methylpiperidine-4-carbonyl)-1,4-dihydropyrrolo[3,4-d]pyrazol-3-yl]-3-methylbutanamide	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.0080	uM
1-(2,6-dichlorophenyl)-6-[[4-(2-hydroxyethoxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[5,4-d]pyrimidin-4-one	1799505: In Vitro Kinase Assay from Article 10.1016/j.chembiol.2005.08.008: “A proteome-wide CDK/CRK-specific kinase inhibitor promotes tumor cell death in the absence of cell cycle progression.”	ic50	0.0090	uM
3-acetyl-7-[[4-(2-methyl-3-propan-2-ylindazol-5-yl)pyrimidin-2-yl]amino]-4-morpholin-4-ylchromen-2-one	1771103: Inhibition of human CDK3/cyclinE using Histone H1 as substrate incubated for 2 hrs by [gamma-33P]-ATP assay	ic50	0.0112	uM
cis-(1S,3R)-3-acetamido-N-[4-(5,5-dimethyl-4,6-dihydropyrrolo[2,1-e]pyrazol-3-yl)-5-fluoro-2-pyridinyl]cyclohexane-1-carboxamide	1684247: Inhibition of CDK3 (unknown origin) in presence of 5 mM ATP	ic50	0.0200	uM
cis-(1S,3R)-3-acetamido-N-[5-chloro-4-(5,5-dimethyl-4,6-dihydropyrrolo[2,1-e]pyrazol-3-yl)-2-pyridinyl]cyclohexane-1-carboxamide	1684247: Inhibition of CDK3 (unknown origin) in presence of 5 mM ATP	ic50	0.0230	uM
(2R,3S)-3-[[6-[(4,6-dimethyl-3-pyridinyl)methylamino]-9-propan-2-ylpurin-2-yl]amino]butan-2-ol	1549289: Inhibition of CDK3 (unknown origin)	ic50	0.0290	uM
methyl (15S,16R,18R)-16-hydroxy-15-methyl-3-oxo-28-oxa-4,14,19-triazaoctacyclo[12.11.2.115,18.02,6.07,27.08,13.019,26.020,25]octacosa-1,6,8,10,12,20,22,24,26-nonaene-16-carboxylate	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.0320	uM
(15S,16S,18R)-16-hydroxy-16-(hydroxymethyl)-15-methyl-28-oxa-4,14,19-triazaoctacyclo[12.11.2.115,18.02,6.07,27.08,13.019,26.020,25]octacosa-1,6,8,10,12,20,22,24,26-nonaen-3-one	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.0370	uM
4-[[4-amino-5-(2-nitrobenzoyl)-1,3-thiazol-2-yl]amino]benzenesulfonamide	745526: Inhibition of CDK3/Cyclin E (unknown origin)-mediated phosphorylation of peptide substrate incubated for 15 mins prior to substrate addition measured after 90 mins by P33-radiolabeled assay	ic50	0.0380	uM
4-(4-methylpiperazin-1-yl)-N-[4-(2-methyl-3-propan-2-ylindazol-5-yl)pyrimidin-2-yl]quinolin-7-amine	1771103: Inhibition of human CDK3/cyclinE using Histone H1 as substrate incubated for 2 hrs by [gamma-33P]-ATP assay	ic50	0.0510	uM
N-[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]piperidine-4-carboxamide	435277: Binding constant for full-length CDK3	kd	0.0560	uM
4-[[5-amino-1-(2,6-difluorobenzoyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide	1890170: Inhibition of CDK3 (unknown origin)	ic50	0.0580	uM
4-[(2,6-dichlorobenzoyl)amino]-N-piperidin-4-yl-1H-pyrazole-5-carboxamide	624828: Binding constant for CDK3 kinase domain	kd	0.0600	uM
3-[3-(2,3-dihydroxypropylamino)phenyl]-4-(5-fluoro-1-methylindol-3-yl)pyrrole-2,5-dione	465269: Inhibition of CDK3	kd	0.0800	uM
1-[4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]-3-[4-[6-(methylamino)pyrimidin-4-yl]oxyphenyl]urea	435277: Binding constant for full-length CDK3	kd	0.0820	uM
cis-(1S,3R)-3-acetamido-N-[5-chloro-4-(4,5,6,7-tetrahydropyrazolo[1,5-a]pyridin-3-yl)-2-pyridinyl]cyclohexane-1-carboxamide	1684247: Inhibition of CDK3 (unknown origin) in presence of 5 mM ATP	ic50	0.0840	uM
cis-(1S,3R)-3-acetamido-N-[4-(4-fluoro-2-methoxyphenyl)-2-pyridinyl]cyclohexane-1-carboxamide	1317373: Inhibition of recombinant human CDK3/cyclin E expressed in baculovirus infected Sf9 insect cells after 80 mins in presence of [33P]ATP by microbeta scintillation counting analysis	ic50	0.0940	uM
(4Z)-4-(2-amino-5-oxo-1H-imidazol-4-ylidene)-2-bromo-1,5,6,7-tetrahydropyrrolo[2,3-c]azepin-8-one	1924337: Inhibition of CDK3/Cyclin E (unknown origin)	ic50	0.1000	uM
5-[2,4-difluoro-3-[[5-[(4-fluorophenyl)carbamoyl]-1H-pyrazol-4-yl]carbamoyl]phenyl]pyridine-2-carboxamide	1732690: Inhibition of CDK3/cyclin E1 (unknown origin) using FAM-labeled peptide and ATP as substrate preincubated for 10 mins followed by substrate addition by mobility shift assay	ic50	0.1130	uM
1-[6-[4-[(2R)-1-hydroxypropan-2-yl]-1,2,4-triazol-3-yl]-2-pyridinyl]-3-pyrazolo[1,5-a]pyridin-2-ylurea	1691913: Inhibition of full length human recombinant CDK3/Cyclin E using histone H1 as substrate incubated for 40 mins in presence of [gamma-33ATP] by radiometric scintillation counting analysis	ic50	0.1167	uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148048: Binding affinity to human CDK3 incubated for 45 mins by Kinobead based pull down assay	kd	0.1336	uM
3-(carbamoylamino)-5-(3-fluorophenyl)-N-[(3S)-piperidin-3-yl]thiophene-2-carboxamide	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.1390	uM
methyl 2-hydroxy-3-[N-[4-[methyl-[2-(4-methylpiperazin-1-yl)acetyl]amino]phenyl]-C-phenylcarbonimidoyl]-1H-indole-6-carboxylate	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.1450	uM
trans-(1S,3S)-3-N-(3-chloro-5-propan-2-ylpyrazolo[1,5-a]pyrimidin-7-yl)cyclopentane-1,3-diamine	2022168: Inhibition of human CDK3/Cyclin E preincubated for 20 mins followed by 32P-ATP addition and measured after 2 hrs	ic50	0.3530	uM
N-[4-[(3R)-3-[[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]amino]piperidine-1-carbonyl]phenyl]prop-2-enamide	1652525: Inhibition of kinase tracer 236 binding to recombinant human full-length N-terminal GST-tagged CDK3/cyclin E1 expressed in baculovirus expression system measured after 1 hr by LanthaScreen Eu Kinase Binding Assay	ic50	0.3660	uM
N-[4-[5-chloro-4-(2-propan-2-ylsulfonylanilino)pyrimidin-2-yl]cyclohexyl]acetamide	2117488: Inhibition of CDK3 (unknown origin) using ULight 4EBP1 peptide as substrate incubated for 2 hrs by FRET assay	ic50	0.3704	uM
[4-amino-2-[[(1S,2S,4R)-2-bicyclo[2.2.1]heptanyl]amino]-1,3-thiazol-5-yl]-(2-nitrophenyl)methanone	1724932: Inhibition of CDK3/cyclinE (unknown origin)	ic50	0.3990	uM
2-(2-chlorophenyl)-5,7-dihydroxy-8-[(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]chromen-4-one	435277: Binding constant for full-length CDK3	kd	0.4100	uM
4-N-(5-cyclopropyl-1H-pyrazol-3-yl)-6-(4-methylpiperazin-1-yl)-2-N-[(3-propan-2-yl-1,2-oxazol-5-yl)methyl]pyrimidine-2,4-diamine	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.4290	uM
N-[5-[(2R)-2-methoxy-2-phenylacetyl]-4,6-dihydro-1H-pyrrolo[3,4-d]pyrazol-3-yl]-4-(4-methylpiperazin-1-yl)benzamide	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.8660	uM
(E)-3-(4-methoxyphenyl)-1-[5-methyl-2-(methylamino)-1,3-thiazol-4-yl]prop-2-en-1-one	1893864: Inhibition of CDK3 in human A549 cells	ic50	0.8700	uM
3-[3-[N-[4-[(dimethylamino)methyl]phenyl]-C-phenylcarbonimidoyl]-2-hydroxy-1H-indol-6-yl]-N-ethylprop-2-ynamide	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.8970	uM
cis-(1R,3S)-3-acetamido-N-[4-(4-fluoro-2-methoxyphenyl)-2-pyridinyl]cyclopentane-1-carboxamide	1317373: Inhibition of recombinant human CDK3/cyclin E expressed in baculovirus infected Sf9 insect cells after 80 mins in presence of [33P]ATP by microbeta scintillation counting analysis	ic50	0.9130	uM
5-chloro-2-N-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-4-N-(5-methyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	0.9420	uM
Sunitinib	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	1.0240	uM
1-[2-[5-[(3-methyloxetan-3-yl)methoxy]benzimidazol-1-yl]quinolin-8-yl]piperidin-4-amine	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	1.0660	uM
trans-(1S,3S)-3-N-[5-(5-chloro-2-methylphenyl)pyrazolo[1,5-a]pyrimidin-7-yl]cyclopentane-1,3-diamine	2022168: Inhibition of human CDK3/Cyclin E preincubated for 20 mins followed by 32P-ATP addition and measured after 2 hrs	ic50	1.0800	uM
3-(1-methylindol-3-yl)-4-[1-[1-(pyridin-2-ylmethyl)piperidin-4-yl]indol-3-yl]pyrrole-2,5-dione	624828: Binding constant for CDK3 kinase domain	kd	1.1000	uM
3-(5-bromo-1-methylindol-3-yl)-4-[6-(hydroxymethyl)-1-benzofuran-3-yl]pyrrole-2,5-dione	415615: Inhibition of CDK3/Cyclin E	ic50	1.2200	uM
1-N-(3-chloro-5-propan-2-ylpyrazolo[1,5-a]pyrimidin-7-yl)cyclobutane-1,3-diamine	2022168: Inhibition of human CDK3/Cyclin E preincubated for 20 mins followed by 32P-ATP addition and measured after 2 hrs	ic50	1.2580	uM
trans-(1S,3S)-3-N-[5-(2-methylphenyl)pyrazolo[1,5-a]pyrimidin-7-yl]cyclopentane-1,3-diamine	2022168: Inhibition of human CDK3/Cyclin E preincubated for 20 mins followed by 32P-ATP addition and measured after 2 hrs	ic50	1.2800	uM
1-cyano-2-methyl-3-[3-[(5-propan-2-ylpyrazolo[1,5-a]pyrimidin-7-yl)amino]cyclobutyl]guanidine	2022168: Inhibition of human CDK3/Cyclin E preincubated for 20 mins followed by 32P-ATP addition and measured after 2 hrs	ic50	1.3500	uM
trans-(1S,3S)-3-N-(5-pentan-3-ylpyrazolo[1,5-a]pyrimidin-7-yl)cyclopentane-1,3-diamine	2022168: Inhibition of human CDK3/Cyclin E preincubated for 20 mins followed by 32P-ATP addition and measured after 2 hrs	ic50	1.4200	uM
4-amino-5-fluoro-3-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-quinolin-2-one	1424945: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.	kd	1.4790	uM
3-acetyl-7-[[5-fluoro-4-(4-fluoro-2-methoxyphenyl)pyrimidin-2-yl]amino]-4-morpholin-4-ylchromen-2-one	1739172: Inhibition of CDK3/Cyclin E (unknown origin) preincubated for 20 mins followed by ATP addition and measured after 120 mins in presence of [33P-gamma] ATP by hotspot kinase assay	ic50	1.5060	uM

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases methylation	4
Benzo(a)pyrene	affects methylation, decreases expression	3
beta-lapachone	increases expression	1
aflatoxin B2	decreases methylation	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
scriptaid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, decreases expression, affects cotreatment	1
belinostat	decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
Vorinostat	decreases expression	1
Arsenic	affects methylation	1
Aspirin	increases expression	1
Cisplatin	increases expression	1
Smoke	decreases expression	1
Sulindac	decreases expression	1
1-Methyl-4-phenylpyridinium	affects expression	1
Reactive Oxygen Species	decreases expression	1
Ritonavir	increases expression	1
Acrylamide	increases expression	1
Chlorodiphenyl (54% Chlorine)	decreases expression	1
p-Chloromercuribenzoic Acid	increases expression, affects cotreatment	1
Nanotubes, Carbon	decreases expression	1

ChEMBL screening assays

330 unique, capped per target: 330 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1047831	Binding	Residual activity of CDK3/Cyclin E at 10 uM by microplate scintillation counting	Substituted 2-arylbenzothiazoles as kinase inhibitors: hit-to-lead optimization. — Bioorg Med Chem

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1N2	Abcam HeLa CDK3 KO	Cancer cell line	Female
CVCL_SI33	HAP1 CDK3 (-) 1	Cancer cell line	Male
CVCL_SI34	HAP1 CDK3 (-) 2	Cancer cell line	Male
CVCL_SI35	HAP1 CDK3 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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