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Tchem
KDM4D
Lysine-specific demethylase 4D

Protein Summary
Description
Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000335080
  • ENSP00000334181
  • ENSG00000186280
  • ENST00000536741
  • ENSP00000460897
  • ENST00000610872
  • ENSP00000482224

Symbol
  • JHDM3D
  • JMJD2D
  • JMJD2D
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
histone modification site profile
0.88
biological process
0.55
tissue sample
0.54
cell line
0.52
cell type or tissue
0.52


Related Tools
GENEVA
GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.
GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
ARCHS4
ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 128.59   (req: < 5)
Gene RIFs: 10   (req: <= 3)
Antibodies: 217   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 128.59   (req: >= 5)
Gene RIFs: 10   (req: > 3)
Antibodies: 217   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 17
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligands: 10
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
Active Ligands (10)
1 – 10 of 10
CHEMBL3769724
chemical structure image
CHEMBL3771198,CHEMBL3771180
chemical structure image
CHEMBL3770740
chemical structure image
CHEMBL3775889
chemical structure image
CHEMBL3775237
chemical structure image
CHEMBL3775612,CHEMBL3774834
chemical structure image
CHEMBL3769511
chemical structure image
CHEMBL3775245
chemical structure image
CHEMBL3774845
chemical structure image
CHEMBL3775431
chemical structure image
Orthologs (5)
1 – 5 of 5
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
lysine demethylase 4D
VGNC:11861
466754
Macaque
lysine-specific demethylase 4D
698455
Mouse
MGI:3606484
244694
Rat
RGD:1591045
689582
Dog
lysine demethylase 4D
485121
Species
Name
OMA
EggNOG
Inparanoid
Chimp
lysine demethylase 4D
Macaque
lysine-specific demethylase 4D
Mouse
Rat
Dog
lysine demethylase 4D
Protein Structure (263 Structures, 1 AlphaFold Model)
RepresentationColor Scheme

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-Q6B0I6-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 263
PDB Structure Id
Ligand
Method
Resolution (Å)
Residues
Fraction of Total Protein
Pub Year
Title
PDB Structure Id
Fraction of Total Protein
Resolution
Pub Year
Pathways (3)
Chromatin modifying enzymes (R-HSA-3247509)

Click on a row in the table to change the structure displayed.

Items per page:
1 – 3 of 3
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Chromatin modifying enzymes
Reactome
Chromatin organization
Reactome
HDMs demethylate histones
Name
Explore in Pharos
Explore in Source
Chromatin modifying enzymes
Chromatin organization
HDMs demethylate histones
Gene Ontology Terms (23)
Items per page:
10
1 – 10 of 10
GO Term
Evidence
Assigned by
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Electronic Annotation (IEA)
Ensembl
Inferred from Electronic Annotation (IEA)
Ensembl
Inferred from Electronic Annotation (IEA)
UniProtKB-KW
Inferred from Electronic Annotation (IEA)
UniProtKB-KW
Protein-Protein Interactions (42)
1 – 10 of 42
TRPC4AP
Tbio
Novelty: 0.02170224
p_int: 0.936359
p_wrong: 0.063641
Score: 0.313
Data Source: BioPlex,STRINGDB
UBAP1
Tbio
Novelty: 0.02276845
Score: 0.832
Data Source: STRINGDB
KDM7A
Tchem
Family: Epigenetic
Novelty: 0.04113733
Score: 0.698
Data Source: STRINGDB
NSD1
Tbio
Family: Epigenetic
Novelty: 0.00495576
Score: 0.695
Data Source: STRINGDB
KDM6B
Tchem
Family: Epigenetic
Novelty: 0.0048959
Score: 0.676
Data Source: STRINGDB
PHF8
Tchem
Family: Epigenetic
Novelty: 0.01946151
Score: 0.67
Data Source: STRINGDB
KDM1A
Tchem
Family: Epigenetic
Novelty: 0.00142673
Score: 0.668
Data Source: STRINGDB
KDM2A
Tchem
Family: Epigenetic
Novelty: 0.01990727
Score: 0.644
Data Source: STRINGDB
JMJD1C
Tbio
Family: Epigenetic
Novelty: 0.02919389
Score: 0.642
Data Source: STRINGDB
PHF2
Tbio
Family: Epigenetic
Novelty: 0.10427439
Score: 0.641
Data Source: STRINGDB
Publication Statistics
PubMed Score  128.59

PubMed score by year
PubTator Score  17.56

PubTator score by year
Amino Acid Sequence
Residue Counts
Protein Sequence
ProtVista Viewer