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CCNB2

gene
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Also known as HsT17299

Summary

CCNB2 (cyclin B2, HGNC:1580) is a protein-coding gene on chromosome 15q22.2, encoding G2/mitotic-specific cyclin-B2 (O95067). Essential for the control of the cell cycle at the G2/M (mitosis) transition.

Cyclin B2 is a member of the cyclin family, specifically the B-type cyclins. The B-type cyclins, B1 and B2, associate with p34cdc2 and are essential components of the cell cycle regulatory machinery. B1 and B2 differ in their subcellular localization. Cyclin B1 co-localizes with microtubules, whereas cyclin B2 is primarily associated with the Golgi region. Cyclin B2 also binds to transforming growth factor beta RII and thus cyclin B2/cdc2 may play a key role in transforming growth factor beta-mediated cell cycle control.

Source: NCBI Gene 9133 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 73 total
  • Druggable target: yes — 17 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_004701

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1580
Approved symbolCCNB2
Namecyclin B2
Location15q22.2
Locus typegene with protein product
StatusApproved
AliasesHsT17299
Ensembl geneENSG00000157456
Ensembl biotypeprotein_coding
OMIM602755
Entrez9133

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 retained_intron

ENST00000288207, ENST00000559301, ENST00000559622, ENST00000561077, ENST00000621385, ENST00000868858, ENST00000930804, ENST00000930805, ENST00000930806, ENST00000930807, ENST00000930808, ENST00000930809, ENST00000930810, ENST00000930811

RefSeq mRNA: 1 — MANE Select: NM_004701 NM_004701

CCDS: CCDS10170

Canonical transcript exons

ENST00000288207 — 9 exons

ExonStartEnd
ENSE000010327105910514659105292
ENSE000010327155910755759107670
ENSE000010327175911669059116926
ENSE000010327185910732259107450
ENSE000010327205912351759123627
ENSE000010327235911471859114876
ENSE000010327245912476759125045
ENSE000035042655911444459114614
ENSE000035791335911722859117368

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 99.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 49.8092 / max 845.8431, expressed in 1576 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
14696440.63361549
1469657.71151214
1469661.4641633

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002399.29gold quality
ventricular zoneUBERON:000305398.66gold quality
secondary oocyteCL:000065598.53gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099196.84gold quality
embryoUBERON:000092296.81gold quality
ganglionic eminenceUBERON:000402396.53gold quality
spermCL:000001996.23gold quality
trabecular bone tissueUBERON:000248396.09gold quality
male germ cellCL:000001595.88gold quality
left testisUBERON:000453394.92gold quality
adult organismUBERON:000702394.58gold quality
right testisUBERON:000453494.42gold quality
testisUBERON:000047393.88gold quality
bone marrowUBERON:000237192.26gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047391.55gold quality
mucosa of transverse colonUBERON:000499189.57gold quality
thymusUBERON:000237089.56gold quality
tongue squamous epitheliumUBERON:000691988.65gold quality
amniotic fluidUBERON:000017388.29gold quality
gingival epitheliumUBERON:000194988.15gold quality
squamous epitheliumUBERON:000691488.04gold quality
cervix squamous epitheliumUBERON:000692288.03gold quality
esophagus squamous epitheliumUBERON:000692087.87gold quality
epithelium of esophagusUBERON:000197687.25gold quality
bone marrow cellCL:000209287.12gold quality
rectumUBERON:000105286.48gold quality
colonic mucosaUBERON:000031786.14gold quality
endometrium epitheliumUBERON:000481185.88gold quality
mucosa of sigmoid colonUBERON:000499385.47gold quality
stromal cell of endometriumCL:000225585.45gold quality

Single-cell (SCXA)

Detected in 17 experiment(s), a significant marker in 14.

ExperimentMarker?Max mean expression
E-GEOD-75140yes1307.30
E-MTAB-10485yes1266.90
E-CURD-112yes1159.75
E-MTAB-11121yes1137.73
E-CURD-79yes1028.93
E-HCAD-56yes872.52
E-MTAB-6379yes646.14
E-HCAD-10yes615.78
E-MTAB-10662yes548.22
E-GEOD-99795yes486.38
E-MTAB-7052yes291.82
E-CURD-114yes139.28
E-HCAD-13yes23.12
E-ANND-3yes6.46
E-MTAB-6911no952.74

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPB, DNMT1, DNMT3B, E2F4, E2F6, EP300, FOXC1, FOXO1, HMGA1, HMGA2, HOXA10, MYBL2, MYC, NFKB, NFYA, NKX2-1, TP53, ZFP42

miRNA regulators (miRDB)

13 targeting CCNB2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7C-3P99.9573.422862
HSA-MIR-806399.9169.763146
HSA-MIR-430799.8270.453374
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-425199.4069.193363
HSA-MIR-316899.0867.751384
HSA-MIR-670-3P99.0368.882404
HSA-MIR-6502-3P97.8665.43569
HSA-MIR-3663-5P97.0164.84713
HSA-MIR-582-3P96.6967.381019
HSA-MIR-4790-5P96.6767.45167
HSA-MIR-10525-3P96.3268.04699
HSA-MIR-1238-3P95.2762.25552

Literature-anchored findings (GeneRIF, showing 33)

  • Overexpression of B-type cyclins alters chromosomal segregation (PMID:11960377)
  • p300 binds to multiple NF-Y trimers to regulate cyclin B2 promoter function (PMID:12482752)
  • cyclin B2 expression in colorectal adenocarcinoma is dependent on NF-Y (PMID:17289878)
  • severe reduction by separate RNA interference of either cyclin B1 or cyclin B2 protein levels results in little or no alteration of the cell cycle and, more specifically, of mitosis progression (PMID:17533373)
  • This gene may be used as a very reliable biomarker of lung adenocarcinoma. (PMID:17549666)
  • The CCNA1, CCNB1, CCNB2, PRM1, and PRM2 messenger RNA transcript ratios were significantly decreased in patients with spermatogenic disorders. Transcript ratios in patients with successful sperm retrieval were higher than with failed sperm retrieval. (PMID:18692784)
  • The radiosensitizing effect of paclitaxel on KB cells may be due to the down-regulated expression of PRC1 and cyclin B2. (PMID:19664331)
  • Data suggest that cyclin A2 helps initiate mitosis, in part through its effects on cyclin B1, and that cyclins B1 and B2 are particularly critical for the maintenance of the mitotic state. (PMID:20660152)
  • The relative expression level of circulating CCNB2 mRNA in cancer patients was significantly higher than that in normal controls and benign diseases group. Circulating CCNB2 mRNA level significantly correlated with cancer stage and metastasis status. (PMID:21161946)
  • Suggest that cytoplasmic CCNB2 may function as an oncogene and could serve as a potential biomarker of unfavorable prognosis over short-term follow-up in breast cancer. (PMID:23282137)
  • Cyclin B1 and cyclin B2 are interchangeable for ability to promote G2 and M transition in HeLa cells. (PMID:24324638)
  • there was no significance in the 5-year overall survival rates among the patients with squamous cell carcinoma between expressing lower and higher level of cyclin B2 mRNA (PMID:24375198)
  • overexpression of CCNB2 protein is associated with clinical progression and poor prognosis in non-small cell lung cancer (PMID:26349989)
  • Data show that the cyclin B2 was overexpressed in bladder cancer tissue. (PMID:26706119)
  • Data show that Islet-1 (ISL1) activated the expression of cyclin B1 (CCNB1), cyclin B2 (CCNB2) and c-myc (c-MYC) genes by binding to the conserved binding sites on their promoters or enhancers. (PMID:27183908)
  • nuclear division cycle 80, cyclin B2 and topoisomerase 2alpha may serve important roles in adrenocortical tumor development. (PMID:30816525)
  • CCNB2 may serve as a prognostic factor and participated in the development and progression and promote cell proliferation and migration through CCNB2/PLK1 pathway in Human Hepatocellular Carcinoma. (PMID:31101236)
  • Cyclin B2 gene is overexpressed in osteosarcoma and associated with poor prognosis outcomes in osteosarcoma patients. (PMID:31278532)
  • Roles of CCNB2 and NKX3-1 in Nasopharyngeal Carcinoma. (PMID:32202926)
  • CCNB2 was upregulated in cortisol-producing adrenocortical carcinoma with TP53 somatic variant. CCNB2 overexpression was associated with atypical mitotic figures. (PMID:32287321)
  • Potential Prognostic Predictors and Molecular Targets for Skin Melanoma Screened by Weighted Gene Co-expression Network Analysis. (PMID:32416689)
  • CCNB2, TOP2A, and ASPM Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis. (PMID:32685486)
  • CDK1, CCNB1, and CCNB2 are Prognostic Biomarkers and Correlated with Immune Infiltration in Hepatocellular Carcinoma. (PMID:32863381)
  • Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndrome. (PMID:34193281)
  • Cyclin B2 (CCNB2) Stimulates the Proliferation of Triple-Negative Breast Cancer (TNBC) Cells In Vitro and In Vivo. (PMID:34354775)
  • CCNB2/SASP/Cathepsin B & PGE2 Axis Induce Cell Senescence Mediated Malignant Transformation. (PMID:34512164)
  • CCNB2 is a novel prognostic factor and a potential therapeutic target in low-grade glioma. (PMID:34908101)
  • CRHBP is degraded via autophagy and exerts anti-hepatocellular carcinoma effects by reducing cyclin B2 expression and dissociating cyclin B2-CDK1 complex. (PMID:35082401)
  • Mad2 promotes Cyclin B2 recruitment to the kinetochore for guiding accurate mitotic checkpoint. (PMID:35384228)
  • Hsa_circ_0000285 knockdown inhibits the progression of hepatocellular carcinoma by sponging miR-582-3p to regulate CCNB2 expression. (PMID:35839486)
  • Cyclin B2 impairs the p53 signaling in nasopharyngeal carcinoma. (PMID:38166895)
  • Prognostic value of cyclin B1 and cyclin B2 expression in breast cancer: A systematic review and updated meta-analysis. (PMID:38241547)
  • Upregulation of CCNB2 and a novel lncRNAs-related risk model predict prognosis in clear cell renal cell carcinoma. (PMID:38300330)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioccnb2ENSDARG00000036180
mus_musculusCcnb2ENSMUSG00000032218
rattus_norvegicusCcnb2-ps2ENSRNOG00000055111
rattus_norvegicusCcnb2ENSRNOG00000063216
drosophila_melanogasterCycBFBGN0000405
caenorhabditis_elegansWBGENE00000865
caenorhabditis_elegansWBGENE00000866
caenorhabditis_eleganscyb-2.2WBGENE00000867

Paralogs (18): CCNE1 (ENSG00000105173), CCNP (ENSG00000105219), CCNJ (ENSG00000107443), CCND1 (ENSG00000110092), CCND3 (ENSG00000112576), CCNG1 (ENSG00000113328), CCNI (ENSG00000118816), CCND2 (ENSG00000118971), CCNA1 (ENSG00000133101), CCNB1 (ENSG00000134057), CCNJL (ENSG00000135083), CCNG2 (ENSG00000138764), CCNA2 (ENSG00000145386), CCNB3 (ENSG00000147082), CCNO (ENSG00000152669), CCNF (ENSG00000162063), CCNE2 (ENSG00000175305), CCNI2 (ENSG00000205089)

Protein

Protein identifiers

G2/mitotic-specific cyclin-B2 — O95067 (reviewed: O95067)

All UniProt accessions (3): O95067, H0YMP3, H1UBN3

UniProt curated annotations — full annotation on UniProt →

Function. Essential for the control of the cell cycle at the G2/M (mitosis) transition.

Subunit / interactions. Interacts with the CDK1 protein kinase to form a serine/threonine kinase holoenzyme complex also known as maturation promoting factor (MPF). The cyclin subunit imparts substrate specificity to the complex.

Similarity. Belongs to the cyclin family. Cyclin AB subfamily.

RefSeq proteins (1): NP_004692* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004367Cyclin_C-domDomain
IPR006671Cyclin_NDomain
IPR013763Cyclin-like_domDomain
IPR036915Cyclin-like_sfHomologous_superfamily
IPR039361CyclinFamily
IPR046965Cyclin_A/B-likeFamily
IPR048258Cyclins_cyclin-boxConserved_site

Pfam: PF00134, PF02984

UniProt features (12 total): modified residue 8, sequence variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95067-F180.140.69

Functional residue map

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

Post-translational modifications (8): 8, 11, 77, 92, 94, 99, 392, 398

Function

Pathways and Gene Ontology

Reactome pathways

24 pathways

IDPathway
R-HSA-156711Polo-like kinase mediated events
R-HSA-162658Golgi Cisternae Pericentriolar Stack Reorganization
R-HSA-2500257Resolution of Sister Chromatid Cohesion
R-HSA-2514853Condensation of Prometaphase Chromosomes
R-HSA-2565942Regulation of PLK1 Activity at G2/M Transition
R-HSA-2980767Activation of NIMA Kinases NEK9, NEK6, NEK7
R-HSA-2995383Initiation of Nuclear Envelope (NE) Reformation
R-HSA-3301854Nuclear Pore Complex (NPC) Disassembly
R-HSA-69273Cyclin A/B1/B2 associated events during G2/M transition
R-HSA-69478G2/M DNA replication checkpoint
R-HSA-8852276The role of GTSE1 in G2/M progression after G2 checkpoint
R-HSA-1640170Cell Cycle
R-HSA-2555396Mitotic Metaphase and Anaphase
R-HSA-2980766Nuclear Envelope Breakdown
R-HSA-2995410Nuclear Envelope (NE) Reassembly
R-HSA-453274Mitotic G2-G2/M phases
R-HSA-68875Mitotic Prophase
R-HSA-68877Mitotic Prometaphase
R-HSA-68882Mitotic Anaphase
R-HSA-68886M Phase
R-HSA-69275G2/M Transition
R-HSA-69278Cell Cycle, Mitotic
R-HSA-69481G2/M Checkpoints
R-HSA-69620Cell Cycle Checkpoints

MSigDB gene sets: 490 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, MODULE_52, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, HORIUCHI_WTAP_TARGETS_DN, GNF2_CENPF, PAL_PRMT5_TARGETS_UP, CROONQUIST_NRAS_SIGNALING_DN, GOBP_T_CELL_HOMEOSTASIS, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GOBP_LYMPHOCYTE_HOMEOSTASIS, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_GROWTH, GNF2_H2AFX, GOBP_THYMUS_DEVELOPMENT, GNF2_RRM2

GO Biological Process (9): G1/S transition of mitotic cell cycle (GO:0000082), in utero embryonic development (GO:0001701), spindle assembly involved in female meiosis I (GO:0007057), G2/MI transition of meiotic cell cycle (GO:0008315), regulation of growth (GO:0040008), T cell homeostasis (GO:0043029), thymus development (GO:0048538), cell division (GO:0051301), mitotic cell cycle phase transition (GO:0044772)

GO Molecular Function (3): cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538), cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (8): cyclin-dependent protein kinase holoenzyme complex (GO:0000307), nucleus (GO:0005634), cytoplasm (GO:0005737), centrosome (GO:0005813), microtubule organizing center (GO:0005815), cytosol (GO:0005829), microtubule cytoskeleton (GO:0015630), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-10 pathways:

CategoryPathways
G2/M Transition4
M Phase3
Mitotic Prophase2
Mitotic Prometaphase2
Nuclear Envelope Breakdown2
Cell Cycle, Mitotic2
Nuclear Envelope (NE) Reassembly1
G2/M Checkpoints1
Mitotic Anaphase1
Mitotic Metaphase and Anaphase1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
mitotic cell cycle2
mitotic cell cycle phase transition1
cell cycle G1/S phase transition1
chordate embryonic development1
spindle assembly involved in female meiosis1
female meiosis I1
meiotic cell cycle phase transition1
cell cycle G2/M phase transition1
meiosis I cell cycle process1
growth1
regulation of biological process1
lymphocyte homeostasis1
hematopoietic or lymphoid organ development1
gland development1
cellular process1
cell cycle phase transition1
mitotic cell cycle process1
cyclin-dependent protein serine/threonine kinase activity1
cyclin-dependent protein kinase regulator activity1
cell adhesion molecule binding1
binding1
serine/threonine protein kinase complex1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
centriole1
microtubule organizing center1
microtubule cytoskeleton1
cytoplasm1
cytoskeleton1

Protein interactions and networks

STRING

3730 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CCNB2CDK1P06493996
CCNB2BUB1O43683970
CCNB2BUB1BO60566915
CCNB2AURKBQ96GD4902
CCNB2BIRC5O15392892
CCNB2CDC6Q99741885
CCNB2CDC20Q12834870
CCNB2PLK1P53350844
CCNB2CDCA8Q53HL2838
CCNB2MAD2L1Q13257836
CCNB2CCNL2Q96S94834
CCNB2MELKQ14680823
CCNB2TOP2AP11388809
CCNB2RRM2P31350808
CCNB2AURKAO14965800

IntAct

95 interactions, top by confidence:

ABTypeScore
CDK2CCNB2psi-mi:“MI:0914”(association)0.860
CDK2CCNB2psi-mi:“MI:0407”(direct interaction)0.860
CDK1CCNB2psi-mi:“MI:0914”(association)0.840
CDKN1ACDK14psi-mi:“MI:0914”(association)0.770
VAPBFAM83Gpsi-mi:“MI:0914”(association)0.730
PKMYT1CCNB2psi-mi:“MI:0914”(association)0.730
FLNACCNB2psi-mi:“MI:0915”(physical association)0.680
CCNB2FLNApsi-mi:“MI:0915”(physical association)0.680
FLNACCNB2psi-mi:“MI:0407”(direct interaction)0.680
CCNB2FLNApsi-mi:“MI:0407”(direct interaction)0.680
FLNACCNB2psi-mi:“MI:0217”(phosphorylation reaction)0.680
FLNACCNB2psi-mi:“MI:0403”(colocalization)0.680
CDKN1BCCNB2psi-mi:“MI:0914”(association)0.670
CCNB2CDKN1Bpsi-mi:“MI:0914”(association)0.670
CRHBPCCNB2psi-mi:“MI:0914”(association)0.640
VAPAFAM83Gpsi-mi:“MI:0914”(association)0.640
CDK2GMNNpsi-mi:“MI:0914”(association)0.640
SKP1MYCBP2psi-mi:“MI:0914”(association)0.640

BioGRID (118): CCNB2 (Affinity Capture-MS), CCNB2 (Affinity Capture-MS), CCNB2 (Affinity Capture-MS), CCNB2 (Affinity Capture-MS), CCNB2 (Affinity Capture-MS), CCNB2 (Affinity Capture-MS), CCNB2 (Co-fractionation), CCNB2 (Co-fractionation), CCNB2 (Co-fractionation), CCNB2 (Co-fractionation), CCNB2 (Co-fractionation), CDK7 (Co-fractionation), DIAPH3 (Co-fractionation), RNASEH2C (Co-fractionation), CCNB2 (Proximity Label-MS)

ESM2 similar proteins: F1N2W9, F1QDI9, F1QMB9, O77689, O93229, O95067, P07818, P13350, P13351, P13952, P14100, P14635, P15206, P24860, P24862, P29332, P30276, P30277, P37882, P37883, P54750, Q01061, Q01064, Q01065, Q01066, Q08301, Q08J23, Q0VGM9, Q1HFZ0, Q1LZG6, Q3TZI6, Q3ZBL9, Q4R7A8, Q60FX9, Q60FY0, Q61481, Q64395, Q6H1L8, Q8RWV3, Q92162

Diamond homologs: A0MEB5, A2YH60, O48790, O77689, O93229, O95067, P04962, P07818, P10815, P13350, P13351, P13952, P14635, P14785, P15206, P18606, P20248, P20439, P24860, P24861, P24862, P24871, P25010, P25011, P25012, P29332, P30183, P30274, P30276, P30277, P30278, P30284, P34800, P34801, P37881, P37882, P37883, P39963, P42524, P43449

SIGNOR signaling

1 interactions.

AEffectBMechanism
NFY“up-regulates quantity by expression”CCNB2“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 76 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:

PathwayPartnersFoldFDR
TP53 Regulates Transcription of Cell Cycle Genes8108.8×1e-12
G1 Phase549.2×1e-06
G1/S Transition846.6×1e-09
Cyclin A/B1/B2 associated events during G2/M transition646.3×3e-07
APC/C-mediated degradation of cell cycle proteins542.0×2e-06
Regulation of mitotic cell cycle542.0×2e-06
Cyclin A:Cdk2-associated events at S phase entry639.8×5e-07
Regulation of APC/C activators between G1/S and early anaphase538.6×4e-06

GO biological processes:

GO termPartnersFoldFDR
G2/M transition of mitotic cell cycle843.8×5e-09
G1/S transition of mitotic cell cycle621.1×5e-05
regulation of mitotic cell cycle521.1×3e-04
Ras protein signal transduction518.0×5e-04
cell division118.9×9e-06
cilium assembly67.8×4e-03
negative regulation of gene expression67.3×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance54
Likely benign5
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1434 predictions. Top by Δscore:

VariantEffectΔscore
15:59107317:TTCA:Tacceptor_loss1.0000
15:59107320:A:AGacceptor_gain1.0000
15:59107320:AG:Aacceptor_gain1.0000
15:59107321:G:GTacceptor_gain1.0000
15:59107321:GG:Gacceptor_gain1.0000
15:59107321:GGT:Gacceptor_gain1.0000
15:59107446:CTAAG:Cdonor_loss1.0000
15:59107447:TAAGG:Tdonor_loss1.0000
15:59107448:AAGGT:Adonor_loss1.0000
15:59107449:AGGTA:Adonor_loss1.0000
15:59107450:GGTA:Gdonor_loss1.0000
15:59107451:GTAAC:Gdonor_loss1.0000
15:59107452:T:Gdonor_loss1.0000
15:59107551:TTATA:Tacceptor_loss1.0000
15:59107553:ATAG:Aacceptor_loss1.0000
15:59107554:TA:Tacceptor_loss1.0000
15:59107555:A:AGacceptor_gain1.0000
15:59107555:AG:Aacceptor_loss1.0000
15:59107556:G:GGacceptor_gain1.0000
15:59107556:GAA:Gacceptor_gain1.0000
15:59107556:GAAA:Gacceptor_gain1.0000
15:59107671:G:Cdonor_loss1.0000
15:59114440:GTAGG:Gacceptor_loss1.0000
15:59114441:TAGG:Tacceptor_loss1.0000
15:59114442:A:Gacceptor_loss1.0000
15:59114442:AG:Aacceptor_gain1.0000
15:59114443:G:GAacceptor_loss1.0000
15:59114443:GG:Gacceptor_gain1.0000
15:59114443:GGGTC:Gacceptor_gain1.0000
15:59114580:T:Gdonor_gain1.0000

AlphaMissense

2614 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:59114793:T:AW172R0.999
15:59114793:T:CW172R0.999
15:59116897:T:CF269L0.999
15:59116899:C:AF269L0.999
15:59116899:C:GF269L0.999
15:59114601:T:CL142P0.998
15:59114795:G:CW172C0.998
15:59114795:G:TW172C0.998
15:59114866:G:CR196P0.998
15:59116748:C:AA219D0.998
15:59116867:T:CF259L0.998
15:59116869:T:AF259L0.998
15:59116869:T:GF259L0.998
15:59114775:C:AR166S0.997
15:59114797:T:CL173P0.997
15:59114824:T:CL182P0.997
15:59116755:G:CK221N0.997
15:59116755:G:TK221N0.997
15:59117319:C:AA309E0.997
15:59114569:C:GC131W0.996
15:59114785:T:CL169P0.996
15:59116715:T:CL208P0.996
15:59116841:A:TE250V0.996
15:59116883:C:AP264H0.996
15:59116898:T:CF269S0.996
15:59116907:G:CR272P0.996
15:59117258:T:GY289D0.996
15:59117271:T:CL293P0.996
15:59117327:G:CA312P0.996
15:59117328:C:AA312D0.996

dbSNP variants (sampled 300 via entrez): RS1000387606 (15:59124600 G>T), RS1000682334 (15:59115216 G>A), RS1000779499 (15:59120579 G>A,C), RS1000985479 (15:59125367 G>C), RS1001003991 (15:59109589 C>A,T), RS1001052816 (15:59115461 G>A), RS1001335774 (15:59112645 G>A), RS1001428349 (15:59118255 T>A), RS1001703439 (15:59112956 C>T), RS1002089577 (15:59123253 C>T), RS1002175248 (15:59108998 A>C), RS1002268489 (15:59108709 T>C), RS1002322962 (15:59114327 T>C), RS1002954529 (15:59106082 G>C), RS1003105295 (15:59117023 C>A,T)

Disease associations

OMIM: gene MIM:602755 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001639_9Metabolite levels1.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004723coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL2094127 (PROTEIN COMPLEX GROUP), CHEMBL3723 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

17 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 198,081 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL189963PALBOCICLIB413,102
CHEMBL2103840DINACICLIB32,257
CHEMBL428690ALVOCIDIB327,781
CHEMBL50QUERCETIN374,559
CHEMBL1230165SILMITASERTIB2593
CHEMBL1276127INDIRUBIN2181
CHEMBL14762SELICICLIB23,787
CHEMBL151LUTEOLIN223,523
CHEMBL2347597ASNUCICLIB2100
CHEMBL31574FISETIN27,745
CHEMBL3545283RIVICICLIB2968
CHEMBL445813AT-751922,614
CHEMBL150KAEMPFEROL125,940
CHEMBL258805SU-9516176
CHEMBL269538HARMINE14,346
CHEMBL296468BMS-38703212,075
CHEMBL412142LADUVIGLUSIB18,434

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

ChEMBL bioactivities

503 potent at pChembl≥5 of 616 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.22IC500.6nMCHEMBL261720
9.22IC500.6nMCHEMBL384350
9.22IC500.6nMCHEMBL426509
9.00IC501nMCHEMBL212552
8.72IC501.9nMCHEMBL377449
8.70IC502nMCHEMBL212299
8.68IC502.1nMCHEMBL361900
8.62IC502.4nMSTAUROSPORINE
8.60IC502.52nMSTAUROSPORINE
8.52IC503nMCHEMBL363607
8.52IC503nMCHEMBL212491
8.52Ki3nMDINACICLIB
8.49IC503.2nMCHEMBL425720
8.49IC503.2nMCHEMBL187395
8.49IC503.2nMCHEMBL364927
8.49IC503.2nMSTAUROSPORINE
8.49IC503.2nMCHEMBL1684800
8.43IC503.7nMCHEMBL370698
8.40Ki4nMASNUCICLIB
8.40IC504nMCHEMBL430653
8.40IC504nMPURVALANOLA
8.35IC504.5nMCHEMBL190643
8.32IC504.8nMCHEMBL363130
8.30Ki5nMCHEMBL5286978
8.30Ki5nMCHEMBL5277074
8.30Ki5nMCHEMBL5286090
8.22IC506nMPURVALANOL B
8.22IC506nMJNJ-7706621
8.22IC506nMCHEMBL310840
8.22Ki6nMCHEMBL5286271
8.22Ki6nMCHEMBL5281179
8.22IC506nMSTAUROSPORINE
8.22IC506nMCHEMBL325023
8.19IC506.4nMJNJ-7706621
8.15IC507nMCHEMBL310567
8.15IC507nMCHEMBL5287128
8.15IC507nMCHEMBL328406
8.10IC508nMCHEMBL363607
8.05IC509nMCHEMBL212833
8.05IC509nMCHEMBL434217
8.02IC509.5nMCHEMBL319467
8.00IC5010nMCHEMBL126997
8.00IC5010nMCHEMBL420463
8.00IC5010nMCHEMBL100012
7.92Ki12nMCHEMBL5277565
7.92IC5012nMCHEMBL318564
7.92IC5012nMSTAUROSPORINE
7.89IC5013nMCHEMBL81211
7.89IC5013nMCHEMBL380301
7.85IC5014nMCHEMBL385478

PubChem BioAssay actives

498 with measured affinity, of 883 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.

CompoundAssayTypeValueUnit
N-[2-methyl-4-(2-pyrrolidin-1-ylethyl)phenyl]-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0006uM
2-[3-methyl-4-[[4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-yl]amino]phenyl]ethanol270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0006uM
5-amino-N-(2,6-difluorophenyl)-3-(4-sulfamoylanilino)-1,2,4-triazole-1-carbothioamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0006uM
N-[2-methyl-4-(2-piperidin-1-ylethyl)phenyl]-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0010uM
N-[2-methyl-4-(2-morpholin-4-ylethyl)phenyl]-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0019uM
4-N-[4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-yl]cyclohexane-1,4-diamine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0020uM
4-[[5-amino-1-(3-fluorothiophene-2-carbonyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0021uM
(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-one1960664: Inhibition of C-terminal His6 tagged human full length CDK1/N-terminal GST-tagged human full length Cyclin B expressed in baculovirus infected Sf21 cells using 5-FAM-QSPKKG-CONH2 as substrate incubated for 60 mins in presence of ATPic500.0024uM
4-[[1-(2,6-difluoro-3-methylbenzoyl)-5-methyl-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0030uM
N-(2-methylphenyl)-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0030uM
2-[(2S)-1-[3-ethyl-7-[(1-oxidopyridin-1-ium-3-yl)methylamino]pyrazolo[1,5-a]pyrimidin-5-yl]piperidin-2-yl]ethanol1940563: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constantki0.0030uM
4-[[5-methyl-1-(2,3,6-trifluorobenzoyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0032uM
4-[[5-amino-2-(2,6-difluorobenzenecarbothioyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0032uM
N-[5-amino-1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-5-[[4-chloro-3-(trifluoromethyl)phenyl]carbamoylamino]-2-methylbenzamide578724: Inhibition of CDK1/cyclin Bic500.0032uM
4-[[5-amino-1-(3,5-dimethylthiophene-2-carbonyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0032uM
5-amino-N-(2,6-difluorophenyl)-3-(4-sulfamoylanilino)-1,2,4-triazole-1-carboxamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0037uM
(2R)-2-[[6-(3-chloroanilino)-9-propan-2-ylpurin-2-yl]amino]-3-methylbutan-1-ol53206: In vitro inhibitory activity against Cyclin-dependent kinase 1-cyclin B complex from starfish oocytesic500.0040uM
5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-N-pyridin-2-yl-1,3-thiazol-2-amine53348: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0040uM
3-[[5-fluoro-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidin-2-yl]amino]benzenesulfonamide1940563: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constantki0.0040uM
4-[[5-amino-1-(thiophene-2-carbonyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0045uM
4-[[5-amino-1-(3-methylthiophene-2-carbonyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide240969: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0048uM
4-[[5-chloro-4-(1-methylpyrazol-4-yl)pyrimidin-2-yl]amino]benzenesulfonamide1940568: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constant incubated for 30 to 60 mins presence of dithiothreitol by Cheng-Prusoff equation analysiski0.0050uM
3-[[5-fluoro-4-(1-methylpyrazol-4-yl)pyrimidin-2-yl]amino]benzenesulfonamide1940568: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constant incubated for 30 to 60 mins presence of dithiothreitol by Cheng-Prusoff equation analysiski0.0050uM
3-[[5-chloro-4-(1-methylpyrazol-4-yl)pyrimidin-2-yl]amino]benzenesulfonamide1940568: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constant incubated for 30 to 60 mins presence of dithiothreitol by Cheng-Prusoff equation analysiski0.0050uM
(4-butoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)-(2,6-difluoro-4-methylphenyl)methanone53347: Inhibition of Cyclin-dependent kinase 1-cyclin Bic500.0060uM
4-[[5-fluoro-4-(1-methylpyrazol-4-yl)pyrimidin-2-yl]amino]benzenesulfonamide1940568: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constant incubated for 30 to 60 mins presence of dithiothreitol by Cheng-Prusoff equation analysiski0.0060uM
5-chloro-4-(1-methylpyrazol-4-yl)-N-(4-methylsulfonylphenyl)pyrimidin-2-amine1940568: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constant incubated for 30 to 60 mins presence of dithiothreitol by Cheng-Prusoff equation analysiski0.0060uM
2-chloro-4-[[2-[[(2R)-1-hydroxy-3-methylbutan-2-yl]amino]-9-propan-2-ylpurin-6-yl]amino]benzoic acid53206: In vitro inhibitory activity against Cyclin-dependent kinase 1-cyclin B complex from starfish oocytesic500.0060uM
1-[3-(2,4-dimethyl-1,3-thiazol-5-yl)-4-oxo-2H-indeno[1,2-c]pyrazol-5-yl]-3-(4-methylpiperazin-1-yl)urea53342: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0060uM
4-[[5-amino-1-(2,6-difluorobenzoyl)-1,2,4-triazol-3-yl]amino]benzenesulfonamide241014: Inhibition of Cyclin B-cyclin-dependent kinase 1ic500.0060uM
(4-butoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)-(2,6-difluoro-4-methoxyphenyl)methanone53347: Inhibition of Cyclin-dependent kinase 1-cyclin Bic500.0070uM
(2R,3R)-3-[[2-[4-(cyclopropylsulfonimidoyl)anilino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]butan-2-ol1921461: Inhibition of CDK1/Cyclin B (unknown origin)ic500.0070uM
5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-N-pyridin-4-yl-1,3-thiazol-2-amine53348: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0070uM
N-(2-chlorophenyl)-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0090uM
4-[[6-(cyclohexylmethoxy)-7H-purin-2-yl]amino]-N-methylbenzenesulfonamide53195: Inhibitory activity against cyclin-dependent kinase 1-cyclin B.ic500.0090uM
4-[[6-(cyclohexylmethoxy)-7H-purin-2-yl]amino]benzenesulfonamide53195: Inhibitory activity against cyclin-dependent kinase 1-cyclin B.ic500.0095uM
1-[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]-3-(2,6-difluorophenyl)urea55520: Inhibitory activity against baculovirus expressed Cyclin dependent kinase 1-cyclinBic500.0100uM
5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-N-pyridin-3-yl-1,3-thiazol-2-amine53348: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0100uM
4-[[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]amino]-N-(2-hydroxyethyl)benzenesulfonamide53348: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0100uM
5-chloro-4-(1,3-dimethylpyrazol-4-yl)-N-(1-methylsulfonylpiperidin-4-yl)pyrimidin-2-amine1940568: Inhibition of CDK1/Cyclin B (unknown origin) assessed as inhibition constant incubated for 30 to 60 mins presence of dithiothreitol by Cheng-Prusoff equation analysiski0.0120uM
5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-N-phenyl-1,3-thiazol-2-amine53348: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0120uM
(4-butoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)-(4-chloro-2,6-difluorophenyl)methanone53347: Inhibition of Cyclin-dependent kinase 1-cyclin Bic500.0130uM
N-(2-bromophenyl)-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0130uM
N-cyclohexyl-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine270821: Inhibition of CDK1/cyclinB by Flashplate assayic500.0140uM
(4-bromo-2,6-difluorophenyl)-(4-butoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)methanone53347: Inhibition of Cyclin-dependent kinase 1-cyclin Bic500.0170uM
3-(3-nitroso-1H-indol-2-yl)-1H-indol-2-ol512487: Inhibition of CDK1/cyclinBic500.0180uM
propan-2-yl N-[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]carbamate55520: Inhibitory activity against baculovirus expressed Cyclin dependent kinase 1-cyclinBic500.0180uM
3-[[6-[[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]amino]-3-pyridinyl]methylamino]-2,2-dimethylpropan-1-ol53348: Inhibition of cyclin-dependent kinase 1-cyclin Bic500.0180uM
1-[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]-3-(4-fluorophenyl)urea55520: Inhibitory activity against baculovirus expressed Cyclin dependent kinase 1-cyclinBic500.0190uM
2-[[[2-[[(2R)-1-hydroxybutan-2-yl]amino]-9-propan-2-ylpurin-6-yl]amino]methyl]phenol53346: Inhibition of recombinant Cyclin-dependent kinase 1-cyclin Bic500.0200uM

CTD chemical–gene interactions

139 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, increases expression, increases methylation, affects cotreatment6
Estradioldecreases expression, increases expression, decreases reaction5
Benzo(a)pyrenedecreases expression4
Fluorouracildecreases expression, affects reaction4
Valproic Aciddecreases expression, affects expression4
Genisteinincreases expression, affects expression, decreases expression4
Cadmiumincreases abundance, increases expression, decreases expression, decreases reaction3
Cisplatinaffects reaction, decreases expression, affects cotreatment, increases expression3
Cyclosporinedecreases expression3
arseniteaffects binding, increases reaction, decreases expression2
cobaltous chloridedecreases expression2
2,3-dimethoxy-1,4-naphthoquinoneincreases expression2
palbociclibdecreases expression2
Irinotecanincreases response to substance, decreases expression2
Resveratrolaffects cotreatment, increases expression, decreases expression2
Fulvestrantdecreases expression, decreases reaction, affects cotreatment2
Copperaffects binding, decreases expression2
Doxorubicinaffects response to substance, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Progesteronedecreases expression, increases expression2
Quercetinincreases expression, decreases expression, affects cotreatment2
Tetrachlorodibenzodioxinaffects expression, increases expression2
Tetradecanoylphorbol Acetateaffects cotreatment, affects expression, increases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Tretinoindecreases expression2
Zincaffects cotreatment, affects expression, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Paclitaxelaffects response to substance, affects cotreatment, decreases expression2
Lithium Chloridedecreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2

ChEMBL screening assays

149 unique, capped per target: 148 binding, 1 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1037380BindingInhibition of human CDK1/cyclin B at 20 uM by FRET assaySynthesis and biological evaluation of p38alpha kinase-targeting dialkynylimidazoles. — Bioorg Med Chem Lett
CHEMBL700201FunctionalIn vitro antiproliferative activity against myeloid leukemia K562 cell linePyrazolo[4,3-d]pyrimidines as new generation of cyclin-dependent kinase inhibitors. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 79

This page pulls from 79 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpatent_compoundpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot