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Center for Computational Systems Medicine
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Kinase Fusion Gene Summary

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Kinase Fusion Gene Sample Information

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Kinase Fusion ORF Analysis

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Kinase Fusion Amino Acid Sequences

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Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase Fusion Protein Functional Features

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Kinase Fusion Protein Structures

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Comparison of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

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pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.

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Ramachandran Plot of Kinase Fusion Protein Structure

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Potential Active Site Information

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Virtual Screening Results

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Kinase-Substrate Information

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Related Drugs with This Kinase Fusion Protein

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Related Disease with This Kinase Fusion Protein

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Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:NEK11_BDH1

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: NEK11_BDH1
KinaseFusionDB ID: KFG4113
FusionGDB2.0 ID: KFG4113
HgeneTgene
Gene symbol

NEK11

BDH1

Gene ID

79858

622

Gene nameNIMA related kinase 113-hydroxybutyrate dehydrogenase 1
Synonyms-BDH|SDR9C1
Cytomap

3q22.1

3q29

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase Nek11NIMA (never in mitosis gene a)- related kinase 11D-beta-hydroxybutyrate dehydrogenase, mitochondrial(R)-3-hydroxybutyrate dehydrogenase3-hydroxybutyrate dehydrogenase (heart, mitochondrial)3-hydroxybutyrate dehydrogenase, type 1epididymis secretory sperm binding proteinshort chain dehydrogenase/red
Modification date2024040320240407
UniProtAcc

Q8NG66

Q02338

Ensembl transtripts involved in fusion geneENST idsENST00000356918, ENST00000383366, 
ENST00000412440, ENST00000429253, 
ENST00000507910, ENST00000508196, 
ENST00000510688, ENST00000510769, 
ENST00000511262, ENST00000426022, 
ENST00000476764, ENST00000358186, 
ENST00000392378, ENST00000392379, 
ENST00000441275, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: NEK11 [Title/Abstract] AND BDH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NEK11(130889731)-BDH1(197241287), # samples:4
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneNEK11

GO:0006468

protein phosphorylation

15161910|19734889

HgeneNEK11

GO:0031573

mitotic intra-S DNA damage checkpoint signaling

15161910

HgeneNEK11

GO:0035556

intracellular signal transduction

15161910


check buttonKinase Fusion gene breakpoints across NEK11 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonKinase Fusion gene breakpoints across BDH1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Kinase Fusion Gene Sample Information

check buttonKinase Fusion gene information.
check button Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceSampleHgeneHchrHbpTgeneTchrTbp
ChimerDB4TCGA-HT-A5RA-01ANEK11chr3

130889731

BDH1chr3

197241287



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Kinase Fusion ORF Analysis


check buttonKinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(amino acids)
ENST00000356918ENST00000392379NEK11chr3130889731BDH1chr31972412874387677

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Kinase Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

>ENST00000356918_ENST00000392379_NEK11_chr3_130889731_BDH1_chr3_197241287_length(amino acids)=677
MFGAMLKFQEAAKCVSGSTAISTYPKTLIARRYVLQQKLGSGSFGTVYLVSDKKAKRGEELKVLKEISVGELNPNETVQANLEAQLLSKL
DHPAIVKFHASFVEQDNFCIITEYCEGRDLDDKIQEYKQAGKIFPENQIIEWFIQLLLGVDYMHERRILHRDLKSKNVFLKNNLLKIGDF
GVSRLLMGSCDLATTLTGTPHYMSPEALKHQGYDTKSDIWSLACILYEMCCMNHAFAGSNFLSIVLKIVEGDTPSLPERYPKELNAIMES
MLNKNPSLRPSAIEILKIPYLDEQLQNLMCRYSEMTLEDKNLDCQKEAAHIINAMQKRIHLQTLRALSEVQKMTPRERMRLRKLQAADEK
ARKLKKIVEEKYEENSKRMQELRSRNFQQLSVDVLHEKTHLKGMEEKEEQPEGRLSCSPQDEDEERWQGREEESDEPTLENLPESQPIPS
MDLHELESIVEDATSDLGYHGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARS
PYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTS

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Multiple Sequence Alignment of All Fusion Protein Isoforms



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Kinase Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:130889731/chr3:197241287)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
NEK11

Q8NG66

BDH1

Q02338

FUNCTION: Protein kinase which plays an important role in the G2/M checkpoint response to DNA damage. Controls degradation of CDC25A by directly phosphorylating it on residues whose phosphorylation is required for BTRC-mediated polyubiquitination and degradation. {ECO:0000269|PubMed:12154088, ECO:0000269|PubMed:19734889, ECO:0000269|PubMed:20090422}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.

check button - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt).
466466466466466466
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote
HgeneNEK11130889731BDH1197241287ENST00000356918121629_2871646DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
HgeneNEK11130889731BDH1197241287ENST00000356918131429_2871483DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
HgeneNEK11130889731BDH1197241287ENST00000356918131629_2871600DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
HgeneNEK11130889731BDH1197241287ENST00000356918131729_2871646DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
HgeneNEK11130889731BDH1197241287ENST00000356918141529_2871471DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
HgeneNEK11130889731BDH1197241287ENST00000356918141829_2871646DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159


check button - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


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Kinase Fusion Protein Structures

check button CIF files of the predicted kinase fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Kinase Fusion protein CIF link (fusion AA seq ID in KinaseFusionDB)HenstTenstHgeneHchrHbpTgeneTchrTbpAA seqLen(AA seq)
PDB file >>>175_NEK11_BDH1ENST00000356918ENST00000392379NEK11chr3130889731BDH1chr3197241287
MFGAMLKFQEAAKCVSGSTAISTYPKTLIARRYVLQQKLGSGSFGTVYLVSDKKAKRGEELKVLKEISVGELNPNETVQANLEAQLLSKL
DHPAIVKFHASFVEQDNFCIITEYCEGRDLDDKIQEYKQAGKIFPENQIIEWFIQLLLGVDYMHERRILHRDLKSKNVFLKNNLLKIGDF
GVSRLLMGSCDLATTLTGTPHYMSPEALKHQGYDTKSDIWSLACILYEMCCMNHAFAGSNFLSIVLKIVEGDTPSLPERYPKELNAIMES
MLNKNPSLRPSAIEILKIPYLDEQLQNLMCRYSEMTLEDKNLDCQKEAAHIINAMQKRIHLQTLRALSEVQKMTPRERMRLRKLQAADEK
ARKLKKIVEEKYEENSKRMQELRSRNFQQLSVDVLHEKTHLKGMEEKEEQPEGRLSCSPQDEDEERWQGREEESDEPTLENLPESQPIPS
MDLHELESIVEDATSDLGYHGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARS
PYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTS
677
3D view using mol* of 175_NEK11_BDH1
PDB file >>>HKFP_254_NEK11_BDH1ENST00000356918ENST00000392379NEK11chr3130889731BDH1chr3197241287
MFGAMLKFQEAAKCVSGSTAISTYPKTLIARRYVLQQKLGSGSFGTVYLVSDKKAKRGEELKVLKEISVGELNPNETVQANLEAQLLSKL
DHPAIVKFHASFVEQDNFCIITEYCEGRDLDDKIQEYKQAGKIFPENQIIEWFIQLLLGVDYMHERRILHRDLKSKNVFLKNNLLKIGDF
GVSRLLMGSCDLATTLTGTPHYMSPEALKHQGYDTKSDIWSLACILYEMCCMNHAFAGSNFLSIVLKIVEGDTPSLPERYPKELNAIMES
MLNKNPSLRPSAIEILKIPYLDEQLQNLMCRYSEMTLEDKNLDCQKEAAHIINAMQKRIHLQTLRALSEVQKMTPRERMRLRKLQAADEK
ARKLKKIVEEKYEENSKRMQELRSRNFQQLSVDVLHEKTHLKGMEEKEEQPEGRLSCSPQDEDEERWQGREEESDEPTLENLPESQPIPS
MDLHELESIVEDATSDLGYHGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARS
PYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTS
677_NEK11_BDH1


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Comparison of Fusion Protein Isoforms

check button Superimpose the 3D Structures Among All Fusion Protein Isoforms
* Download the pdb file and open it from the molstar online viewer.

check button Comparison of the Secondary Structures of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

NEK11_BDH1 does not have any known PDB structures.

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pLDDT score distribution

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
* The blue color at the bottom marks the best active site residues.
175_NEK11_BDH1.png
all structure sitemap plddt 175_NEK11_BDH1.png
175_NEK11_BDH1.png
all structure sitemap plddt2 175_NEK11_BDH1.png


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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Kinase Fusion AA seq ID in KinaseFusionDBSite scoreSizeDscoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues

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Ramachandran Plot of Kinase Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

175_NEK11_BDH1_ramachandran.png
all structure NEK11-BDH1

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Virtual Screening Results


check button Distribution of the average docking score across all approved kinase inhibitors.
Distribution of the number of occurrence across all approved kinase inhibitors.
5'-kinase fusion protein case
all structure NEK11-BDH1
3'-kinase fusion protein case

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check button Drug information from DrugBank of the top 20 interacting small molecules.
* The detailed information of individual kinase inhibitors are available in the download page.
Fusion gene name infoDrugDocking scoreGlide g scoreGlide energy
175_NEK11_BDH1-DOCK_HTVS_1-001Tepotinib-9.2291-9.2302-49.9755
175_NEK11_BDH1-DOCK_HTVS_1-001Sorafenib-8.60101-8.61311-57.6941
175_NEK11_BDH1-DOCK_HTVS_1-001Sorafenib-8.60101-8.61311-57.6941
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.16617-8.96367-39.9826
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.16617-8.96367-39.9826
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.16617-8.96367-39.9826
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.16617-8.96367-39.9826
175_NEK11_BDH1-DOCK_HTVS_1-001Regorafenib-8.07986-8.07986-58.5201
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.00098-8.33228-38.3266
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.00098-8.33228-38.3266
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.00098-8.33228-38.3266
175_NEK11_BDH1-DOCK_HTVS_1-001Avapritinib-8.00098-8.33228-38.3266
175_NEK11_BDH1-DOCK_HTVS_1-001Asciminib-8.00032-8.46532-51.245
175_NEK11_BDH1-DOCK_HTVS_1-001Asciminib-7.6680600000000005-8.13306-41.8124
175_NEK11_BDH1-DOCK_HTVS_1-001Asciminib-7.5782300000000005-7.941330000000001-45.2127
175_NEK11_BDH1-DOCK_HTVS_1-001Ribociclib-7.566730000000001-7.635730000000001-42.6705
175_NEK11_BDH1-DOCK_HTVS_1-001Ribociclib-7.566730000000001-7.635730000000001-42.6705
175_NEK11_BDH1-DOCK_HTVS_1-001Tivozanib-7.33778-7.33778-51.4035
175_NEK11_BDH1-DOCK_HTVS_1-001Palbociclib-7.2800899999999995-7.68699-43.7065
175_NEK11_BDH1-DOCK_HTVS_1-001Palbociclib-7.2800899999999995-7.68699-43.7065

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Kinase-Substrate Information of NEK11_BDH1


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
NEK11Q8NG66humanCDC25AP30304S82GssEstDsGFCLDsP
NEK11Q8NG66humanBLMP54132S338kEDVLSTskDLLskPBLM_N
NEK11Q8NG66humanCDC25AP30304S88DsGFCLDsPGPLDSKM-inducer_phosp
NEK11Q8NG66humanCDC25AP30304S79QRMGssEstDsGFCL


check button Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

check button Enriched GO biological processes of the phosphorylation target genes of the kinase
KinaseGOIDGO termP.adjust
NEK11IDDescription0.00e+00
NEK11GO:0000079regulation of cyclin-dependent protein serine/threonine kinase activity8.62e-04
NEK11GO:1904029regulation of cyclin-dependent protein kinase activity8.62e-04
NEK11GO:0010389regulation of G2/M transition of mitotic cell cycle8.62e-04
NEK11GO:1902749regulation of cell cycle G2/M phase transition8.62e-04
NEK11GO:0000086G2/M transition of mitotic cell cycle1.01e-03
NEK11GO:0044839cell cycle G2/M phase transition1.03e-03
NEK11GO:0071478cellular response to radiation1.20e-03
NEK11GO:0071900regulation of protein serine/threonine kinase activity2.61e-03
NEK11GO:0071214cellular response to abiotic stimulus2.87e-03
NEK11GO:0104004cellular response to environmental stimulus2.87e-03
NEK11GO:1901990regulation of mitotic cell cycle phase transition2.95e-03
NEK11GO:0009314response to radiation3.94e-03
NEK11GO:1901987regulation of cell cycle phase transition4.07e-03
NEK11GO:0044772mitotic cell cycle phase transition4.07e-03
NEK11GO:1901993regulation of meiotic cell cycle phase transition6.31e-03
NEK11GO:0072711cellular response to hydroxyurea6.31e-03
NEK11GO:0090657telomeric loop disassembly6.31e-03
NEK11GO:0072710response to hydroxyurea6.50e-03
NEK11GO:0044771meiotic cell cycle phase transition6.65e-03
NEK11GO:0001325formation of extrachromosomal circular DNA6.65e-03
NEK11GO:0090656t-circle formation6.65e-03
NEK11GO:0090737telomere maintenance via telomere trimming6.65e-03
NEK11GO:0051782negative regulation of cell division7.20e-03
NEK11GO:0000729DNA double-strand break processing8.19e-03
NEK11GO:0006268DNA unwinding involved in DNA replication8.19e-03
NEK11GO:0051446positive regulation of meiotic cell cycle1.01e-02
NEK11GO:0010165response to X-ray1.01e-02
NEK11GO:0010971positive regulation of G2/M transition of mitotic cell cycle1.01e-02
NEK11GO:1902751positive regulation of cell cycle G2/M phase transition1.08e-02
NEK11GO:0007095mitotic G2 DNA damage checkpoint signaling1.16e-02
NEK11GO:0071312cellular response to alkaloid1.16e-02
NEK11GO:0033260nuclear DNA replication1.22e-02
NEK11GO:0044786cell cycle DNA replication1.30e-02
NEK11GO:0090329regulation of DNA-templated DNA replication1.35e-02
NEK11GO:0031297replication fork processing1.35e-02
NEK11GO:0045910negative regulation of DNA recombination1.35e-02
NEK11GO:0044818mitotic G2/M transition checkpoint1.39e-02
NEK11GO:0045005DNA-templated DNA replication maintenance of fidelity1.43e-02
NEK11GO:0051445regulation of meiotic cell cycle1.62e-02
NEK11GO:0010972negative regulation of G2/M transition of mitotic cell cycle1.62e-02
NEK11GO:0071479cellular response to ionizing radiation1.62e-02
NEK11GO:1902750negative regulation of cell cycle G2/M phase transition1.62e-02
NEK11GO:0032508DNA duplex unwinding1.79e-02
NEK11GO:0044773mitotic DNA damage checkpoint signaling1.80e-02
NEK11GO:0032392DNA geometric change1.80e-02
NEK11GO:2000243positive regulation of reproductive process1.80e-02
NEK11GO:0044774mitotic DNA integrity checkpoint signaling1.80e-02
NEK11GO:0034644cellular response to UV1.81e-02
NEK11GO:0071103DNA conformation change1.81e-02

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Related Drugs to NEK11_BDH1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

check button Distribution of the number of studies mentioning NEK11-BDH1 and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1Fusion gene - drug pair 2PMIDPublication dateDOIStudy title

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Related Diseases to NEK11_BDH1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)
MeSH IDMeSH term

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource


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Clinical Trials of the Found Drugs/Small Molecules


check button Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

check button Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion GeneKinase InhibitorNCT IDStudy StatusPhasesDisease# EnrolmentDate