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Center for Computational Systems Medicine
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Protein Summary

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AS Summary

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Protein Functional Features

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Gene Isoform Structures and Expression Levels

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Protein Structures

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pLDDT Score Distribution

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Ramachandran Plot of Protein Structures

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Potential Active Site Information

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Protein Structure and Feature Comparision

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Protein-Protein Interaction

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Related Drugs

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Related Diseases

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Clinically Important Variants

Protein:KDM2A

Protein Summary

check button Gene summary
Gene name: KDM2A
ASpdb.0 ID: 22992
Gene
Gene symbol

KDM2A

Gene ID

22992

Gene namelysine demethylase 2A
SynonymsCXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA
Cytomap

11q13.2

Type of geneprotein-coding
Descriptionlysine-specific demethylase 2ACXXC-type zinc finger protein 8F-box and leucine-rich repeat protein 11F-box/LRR-repeat protein 11[Histone-H3]-lysine-36 demethylase 1AjmjC domain-containing histone demethylation protein 1Ajumonji C domain-containing h
Modification date20240305
UniProtAcc

Q9Y2K7


check button Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
GeneKDM2A

GO:0005654

nucleoplasm

-

GeneKDM2A

GO:0008270

zinc ion binding

29276034

GeneKDM2A

GO:0045322

unmethylated CpG binding

29276034



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
Q9Y2K7-1Q9Y2K7-1_2yu2_A.pdb2YU2X-ray2.7A34517

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
Q9Y2K7KDM2AQ9Y2K7-1Q9Y2K7-211628561306Deletionnonenone00
Q9Y2K7KDM2AQ9Y2K7-1Q9Y2K7-31162782774782SubstitutionREKENNPSGLRQETLDKN774782
Q9Y2K7KDM2AQ9Y2K7-1Q9Y2K7-311627827831162Deletionnonenone782782
Q9Y2K7KDM2AQ9Y2K7-1Q9Y2K7-411626201542Deletionnonenone00
Q9Y2K7KDM2AQ9Y2K7-1Q9Y2K7-511627231439Deletionnonenone00
Q9Y2K7KDM2AQ9Y2K7-1Q9Y2K7-51162723440492SubstitutionDPQCAPRKDRQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVMCSGRFQNIQVNPDFPRGRISNSFRRTSSTENKTKTLGKLHQEPRQLQSDGKR153

check buttonMultiple sequence alignment of our canonical and alternatively spliced KDM2A

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of KDM2A
UniProt-idENSGENSTENSP
Q9Y2K7-1ENSG00000173120.15ENST00000529006.7ENSP00000432786.1
Q9Y2K7-3ENSG00000173120.15ENST00000398645.6ENSP00000381640.2
Q9Y2K7-5ENSG00000173120.15ENST00000530342.2ENSP00000435776.1

UniProt-idNM IDNP ID
Q9Y2K7-1NM_012308.2NP_036440.1
Q9Y2K7-2XM_011544861.1XP_011543163.1
Q9Y2K7-5NM_001256405.1NP_001243334.1

check buttonAmino acid sequences of our canonical and alternatively spliced KDM2A
accession_idProtein sequence
Q9Y2K7-1MEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLHTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPD
PDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKES
QTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIEL
KQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYNIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKEFQKESLS
MDLELNGLESGNGDEEAVDREPRRLSSRRSVLTSPVANGVNLDYDGLGKTCRSLPSLKKTLAGDSSSDCSRGSHNGQVWDPQCAPRKDRQ
VHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELANSDPKLALTGVPIVQWPKRDKLKFPTRPKVRVPTIPITKP
HTMKPAPRLTPVRPAAASPIVSGARRRRVRCRKCKACVQGECGVCHYCRDMKKFGGPGRMKQSCVLRQCLAPRLPHSVTCSLCGEVDQNE
ETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQEDSSEKAQKRKMEESDEEAVQAKVLRPLRSCDEPLTPPPHSPT
SMLQLIHDPVSPRGMVTRSSPGAGPSDHHSASRDERFKRRQLLRLQATERTMVREKENNPSGKKELSEVEKAKIRGSYLTVTLQRPTKEL
HGTSIVPKLQAITASSANLRHSPRVLVQHCPARTPQRGDEEGLGGEEEEEEEEEEEDDSAEEGGAARLNGRGSWAQDGDESWMQREVWMS
VFRYLSRRELCECMRVCKTWYKWCCDKRLWTKIDLSRCKAIVPQALSGIIKRQPVSLDLSWTNISKKQLTWLVNRLPGLKDLLLAGCSWS
AVSALSTSSCPLLRTLDLRWAVGIKDPQIRDLLTPPADKPGQDNRSKLRNMTDFRLAGLDITDATLRLIIRHMPLLSRLDLSHCSHLTDQ
Q9Y2K7-2MQLKIYNIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKEFQKESLSMDLELNGLESGNGDEEAVDREPRRLSSRRSVLTSPV
ANGVNLDYDGLGKTCRSLPSLKKTLAGDSSSDCSRGSHNGQVWDPQCAPRKDRQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDED
ALIADVKILLEELANSDPKLALTGVPIVQWPKRDKLKFPTRPKVRVPTIPITKPHTMKPAPRLTPVRPAAASPIVSGARRRRVRCRKCKA
CVQGECGVCHYCRDMKKFGGPGRMKQSCVLRQCLAPRLPHSVTCSLCGEVDQNEETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEEL
PNCWECPKCYQEDSSEKAQKRKMEESDEEAVQAKVLRPLRSCDEPLTPPPHSPTSMLQLIHDPVSPRGMVTRSSPGAGPSDHHSASRDER
FKRRQLLRLQATERTMVREKENNPSGKKELSEVEKAKIRGSYLTVTLQRPTKELHGTSIVPKLQAITASSANLRHSPRVLVQHCPARTPQ
RGDEEGLGGEEEEEEEEEEEDDSAEEGGAARLNGRGSWAQDGDESWMQREVWMSVFRYLSRRELCECMRVCKTWYKWCCDKRLWTKIDLS
RCKAIVPQALSGIIKRQPVSLDLSWTNISKKQLTWLVNRLPGLKDLLLAGCSWSAVSALSTSSCPLLRTLDLRWAVGIKDPQIRDLLTPP
ADKPGQDNRSKLRNMTDFRLAGLDITDATLRLIIRHMPLLSRLDLSHCSHLTDQSSNLLTAVGSSTRYSLTELNMAGCNKLTDQTLIYLR
Q9Y2K7-3MEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLHTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPD
PDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKES
QTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIEL
KQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYNIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKEFQKESLS
MDLELNGLESGNGDEEAVDREPRRLSSRRSVLTSPVANGVNLDYDGLGKTCRSLPSLKKTLAGDSSSDCSRGSHNGQVWDPQCAPRKDRQ
VHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELANSDPKLALTGVPIVQWPKRDKLKFPTRPKVRVPTIPITKP
HTMKPAPRLTPVRPAAASPIVSGARRRRVRCRKCKACVQGECGVCHYCRDMKKFGGPGRMKQSCVLRQCLAPRLPHSVTCSLCGEVDQNE
ETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQEDSSEKAQKRKMEESDEEAVQAKVLRPLRSCDEPLTPPPHSPT
Q9Y2K7-4MKPAPRLTPVRPAAASPIVSGARRRRVRCRKCKACVQGECGVCHYCRDMKKFGGPGRMKQSCVLRQCLAPRLPHSVTCSLCGEVDQNEET
QDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQEDSSEKAQKRKMEESDEEAVQAKVLRPLRSCDEPLTPPPHSPTSM
LQLIHDPVSPRGMVTRSSPGAGPSDHHSASRDERFKRRQLLRLQATERTMVREKENNPSGKKELSEVEKAKIRGSYLTVTLQRPTKELHG
TSIVPKLQAITASSANLRHSPRVLVQHCPARTPQRGDEEGLGGEEEEEEEEEEEDDSAEEGGAARLNGRGSWAQDGDESWMQREVWMSVF
RYLSRRELCECMRVCKTWYKWCCDKRLWTKIDLSRCKAIVPQALSGIIKRQPVSLDLSWTNISKKQLTWLVNRLPGLKDLLLAGCSWSAV
SALSTSSCPLLRTLDLRWAVGIKDPQIRDLLTPPADKPGQDNRSKLRNMTDFRLAGLDITDATLRLIIRHMPLLSRLDLSHCSHLTDQSS
Q9Y2K7-5MCSGRFQNIQVNPDFPRGRISNSFRRTSSTENKTKTLGKLHQEPRQLQSDGKRKILLEELANSDPKLALTGVPIVQWPKRDKLKFPTRPK
VRVPTIPITKPHTMKPAPRLTPVRPAAASPIVSGARRRRVRCRKCKACVQGECGVCHYCRDMKKFGGPGRMKQSCVLRQCLAPRLPHSVT
CSLCGEVDQNEETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQEDSSEKAQKRKMEESDEEAVQAKVLRPLRSCD
EPLTPPPHSPTSMLQLIHDPVSPRGMVTRSSPGAGPSDHHSASRDERFKRRQLLRLQATERTMVREKENNPSGKKELSEVEKAKIRGSYL
TVTLQRPTKELHGTSIVPKLQAITASSANLRHSPRVLVQHCPARTPQRGDEEGLGGEEEEEEEEEEEDDSAEEGGAARLNGRGSWAQDGD
ESWMQREVWMSVFRYLSRRELCECMRVCKTWYKWCCDKRLWTKIDLSRCKAIVPQALSGIIKRQPVSLDLSWTNISKKQLTWLVNRLPGL
KDLLLAGCSWSAVSALSTSSCPLLRTLDLRWAVGIKDPQIRDLLTPPADKPGQDNRSKLRNMTDFRLAGLDITDATLRLIIRHMPLLSRL
DLSHCSHLTDQSSNLLTAVGSSTRYSLTELNMAGCNKLTDQTLIYLRRIANVTLIDLRGCKQITRKACEHFISDLSINSLYCLSDEKLIQ

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
KDM2A (go to UniProt):Q9Y2K7

check buttonRetention analysis result of 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.
- Retained protein feature among the 13 regional features.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
Q9Y2K7Domain148316Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538Type=Deletion;Start=1;End=306
Q9Y2K7Domain148316Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538Type=Deletion;Start=1;End=542
Q9Y2K7Domain148316Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00538Type=Deletion;Start=1;End=439
Q9Y2K7Domain889936Note=F-boxType=Deletion;Start=783;End=1162
Q9Y2K7Repeat961982Note=LRR 1Type=Deletion;Start=783;End=1162
Q9Y2K7Repeat9841010Note=LRR 2Type=Deletion;Start=783;End=1162
Q9Y2K7Repeat10481073Note=LRR 3Type=Deletion;Start=783;End=1162
Q9Y2K7Repeat10741103Note=LRR 4Type=Deletion;Start=783;End=1162
Q9Y2K7Repeat11041128Note=LRR 5Type=Deletion;Start=783;End=1162
Q9Y2K7Repeat11291156Note=LRR 6Type=Deletion;Start=783;End=1162
Q9Y2K7Region367389Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=542
Q9Y2K7Region367389Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=439
Q9Y2K7Region532557Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=542
Q9Y2K7Region704789Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Substitution;Start=774;End=782
Q9Y2K7Region704789Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=783;End=1162
Q9Y2K7Region839887Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=783;End=1162
Q9Y2K7Compositional bias373387Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=542
Q9Y2K7Compositional bias373387Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=1;End=439
Q9Y2K7Compositional bias748789Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Substitution;Start=774;End=782
Q9Y2K7Compositional bias748789Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=783;End=1162
Q9Y2K7Compositional bias852871Note=Acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=783;End=1162


Gene Isoform Structures and Expression Levels for KDM2A

check buttonGene structures of our canonical and alternative spliced genes of KDM2A
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
gene isoform structure of KDM2A

check button Expression levels of gene isoforms across GTEx.
gtex expression

check button Expression levels of gene isoforms across TCGA.
tcga expression


Protein Structures

check button PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the 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.
3D view using mol* of Q9Y2K7-1
3D view using mol* of Q9Y2K7-2
3D view using mol* of Q9Y2K7-3
3D view using mol* of Q9Y2K7-4
3D view using mol* of Q9Y2K7-5


pLDDT Score Distribution

check button pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
pLDDT distribution across the protein length of Q9Y2K7-1
all structure
pLDDT distribution across the protein length of Q9Y2K7-2
all structure
pLDDT distribution across the protein length of Q9Y2K7-3
all structure
pLDDT distribution across the protein length of Q9Y2K7-4
all structure
pLDDT distribution across the protein length of Q9Y2K7-5
all structure


Ramachandran Plot of Protein Structures


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.
Ramachandran plot of Q9Y2K7-1
all structure
Ramachandran plot of Q9Y2K7-2
all structure
Ramachandran plot of Q9Y2K7-3
all structure

Potential Active Site Information


check button The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.
UniProt-idSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
Q9Y2K7-11.0481221.067748.4260.640.760.9020.3861.0110.3821.17485,147,149,150,154,155,158,159,161,164,165,170,171
,175,178,179,193,195,196,197,198,361,515,516,517,5
18,519,521,522,523,524
Q9Y2K7-20.9971221.054297.0380.6250.6240.8250.8430.81.0540.5431,2,3,4,5,6,9,19,20,23,26,27,29,30,33,34,150,151,1
53,154,155,157,158,161,208,210
Q9Y2K7-31.0324231.0261183.0070.4960.7470.9560.4881.1090.4411.01932,33,34,35,36,37,106,107,108,109,110,111,113,114,
115,116,117,118,120,142,143,144,145,146,147,185,18
6,187,188,191,196,199,201,203,207,208,209,210,211,
212,213,214,215,220,222,229,231,244,247,248,251,25
2,253,254,255,278,284,286,288,296,297,298,311,312,
314,315,318,320,322,323,324,325,326,327,328,329,33
0,331,477
Q9Y2K7-40.9943321.0121423.7930.5770.6890.8790.4961.0480.4730.94623,26,27,28,33,34,37,40,42,43,44,45,47,60,61,63,64
,66,67,68,70,101,119,120,121,122,123,124,128,129,3
49,350,353,379,380,381,383,384,385,401,404,405,408
,409,411,413,424,425,426,428,429,432,433,435,436,4
55
Q9Y2K7-50.9821171.039323.7920.6790.6040.7740.4830.8060.5980.9158,9,10,11,12,14,15,60,61,63,64,65,67,68,70,72,73,7
4,75,76,77,78

Protein Structure and Feature Comparision


check button Protein Structure Comparision Using Template Modeling Scores (TM-score).
all structure

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)
3D view using mol* of Q9Y2K7-1_Q9Y2K7-1_2yu2_A.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of Q9Y2K7-1_2yu2_A_Q9Y2K7-2.pdb
3D view using mol* of Q9Y2K7-1_2yu2_A_Q9Y2K7-3.pdb
3D view using mol* of Q9Y2K7-1_2yu2_A_Q9Y2K7-4.pdb
3D view using mol* of Q9Y2K7-1_2yu2_A_Q9Y2K7-5.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of Q9Y2K7-1_Q9Y2K7-2.pdb
3D view using mol* of Q9Y2K7-1_Q9Y2K7-3.pdb
3D view using mol* of Q9Y2K7-1_Q9Y2K7-4.pdb
3D view using mol* of Q9Y2K7-1_Q9Y2K7-5.pdb

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/Q9Y2K7-1_vs_Q9Y2K7-2.png
all structure<
./stats/secondary_structure/figure/Q9Y2K7-1_vs_Q9Y2K7-3.png
all structure<
./stats/secondary_structure/figure/Q9Y2K7-1_vs_Q9Y2K7-4.png
all structure<
./stats/secondary_structure/figure/Q9Y2K7-1_vs_Q9Y2K7-5.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/Q9Y2K7-1_vs_Q9Y2K7-2.png
all structure<
./stats/relative_asa/Q9Y2K7-1_vs_Q9Y2K7-3.png
all structure<
./stats/relative_asa/Q9Y2K7-1_vs_Q9Y2K7-4.png
all structure<
./stats/relative_asa/Q9Y2K7-1_vs_Q9Y2K7-5.png
all structure<


Protein-Protein Interaction


check button Interactors from UniProt.
Accession_idSubsectionStartEndFuncitonal featureSplicing information


check button Interactors from STRING.
Gene nameInteractors


Related Drugs to KDM2A


check button Drugs targeting this gene/protein.
(DrugBank)
UniProt accessionGene nameDrugBank IDDrug nameDrug groupActions

Related Diseases to KDM2A


check button Previous studies relating to the alternative splicing of KDM2A and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term


Clinically important variants in KDM2A


check button (ClinVar, 04/20/2024)
accession_iduniprot_idgene_nameTypeVariantClinical_significance