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PsychedeliaDokholyan Laboratory
TargetEnzymes

Lysine-specific demethylase 4A

Named enzymes, including the metabolising cytochromes and the monoamine oxidases.

Measurements
5
Compounds
5
Binding constants
0
Median pX
—

I · Identity

What this target is

Its function as UniProt states it, where in a cell the protein is found, and which cell types and tissues transcribe its gene.

Protein

KDM4A_HUMANKDM4AHomo sapiens

Lysine-specific demethylase 4A

Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code16603238,26741168,21768309. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'16603238,26741168,21768309. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues16603238,26741168,21768309. Demethylation of Lys residue generates formaldehyde and succinate16603238. Also able to demethylate histone H1-4 methylated at 'Lys-26' (H1.4K26me1, H1.4K26me2 and H1.4K26me3)19144645,30156264. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively16024779
Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain

Quoted from UniProt’s FUNCTION annotation for O75164 (reviewed). The superscript numbers are UniProt’s own PubMed citations, kept in the sentence and in order, each linking to the paper it names.

What it acts with

STRING’s highest-confidence human functional partners. The combined score mixes several kinds of evidence, so each channel is shown separately — a partner supported by experiment is a different claim from one supported only by text mining, and for a receptor this is where its coupling appears as evidence rather than as assertion.

PartnerCombinedExperimentDatabaseText mining
H3C120.9990.9520.4000.972
H3-40.9980.9490.5000.958
H3-3B0.9980.9490.0000.972
H3C130.9970.9050.4000.958
H3-20.9950.9050.0000.958
H3-50.9950.9050.0000.958
H4C60.9930.9630.5000.657
H3C10.9750.9720.0000.102
KDM1A0.9660.0910.5000.927
H1-40.9520.9000.0000.540

Where it sits in the cell

  • Nucleoli fibrillar center
  • Nucleoplasmadditional

Human Protein Atlas, by antibody immunofluorescence in cell lines — a different assay from the expression figures below, which are RNA.

UniProt, curated Nucleus

Expression by cell type

Single cell type RNA, the 10 highest of those the Human Protein Atlas reports for this gene. Transcript, not protein, and a cell type rather than a tissue.

  • Choroid plexus epithelial cells39.2 nCPM
  • Ependymal cells36 nCPM
  • Oligodendrocytes34.7 nCPM
  • Brain inhibitory neurons31.4 nCPM
  • Microglia30.5 nCPM
  • Oligodendrocyte progenitor cells29.1 nCPM
  • Brain excitatory neurons28.5 nCPM
  • Bergmann glia26.8 nCPM
  • Astrocytes26.5 nCPM
  • Other brain neurons21 nCPM

II · Anatomy

Where the gene is transcribed

The same two atlases the compound plates use, asked about this gene alone. Brain on the left, peripheral and autonomic tissues on the right.

Brain

cerebral cortex — 10.8 nTPM, from KDM4Acerebellum — 15.1 nTPM, from KDM4Ahippocampal formation — 7.6 nTPM, from KDM4Aamygdala — 7.3 nTPM, from KDM4Ahypothalamus — 7.1 nTPM, from KDM4Athalamus — no resolved target expressed herebasal ganglia — 9.8 nTPM, from KDM4Amedulla oblongata — no resolved target expressed here

basal ganglia: drawn as the caudate nucleus, putamen and globus pallidus.

Measured but not drawn — this anatomogram has no outline for them: retina 18.2, pituitary gland 10.4, spinal cord 7.6, midbrain 7.0.

Body

heart — 9.3 nTPM, from KDM4Asmooth muscle — 13.9 nTPM, from KDM4Alung — 13.8 nTPM, from KDM4Aliver — 14.0 nTPM, from KDM4Akidney — 11.9 nTPM, from KDM4Astomach — 13.6 nTPM, from KDM4Aduodenum — 26.3 nTPM, from KDM4Asmall intestine — 21.3 nTPM, from KDM4Acolon — 16.9 nTPM, from KDM4Aadrenal gland — 19.4 nTPM, from KDM4Athyroid gland — 16.2 nTPM, from KDM4Apancreas — 11.9 nTPM, from KDM4Aurinary bladder — 12.8 nTPM, from KDM4Askeletal muscle — 10.3 nTPM, from KDM4Aspleen — 13.1 nTPM, from KDM4Asalivary gland — 12.8 nTPM, from KDM4A
026 nTPM

Square-root ramp · shared scale across both plates

Shading is transcript level — not affinity, and not affinity combined with expression. Outlined but unshaded organs hold none of KDM4A transcript above the atlas’s detection threshold. Anatomy from EMBL-EBI Anatomogram (Apache License 2.0); regions identified by Uberon (uberon.org), CC BY 3.0.

Brain · 10

  • retina18.2 nTPM
  • cerebellum15.1 nTPM
  • cerebral cortex10.8 nTPM
  • pituitary gland10.4 nTPM
  • basal ganglia9.8 nTPM
  • hippocampal formation7.6 nTPM
  • spinal cord7.6 nTPM
  • amygdala7.3 nTPM
  • hypothalamus7.1 nTPM
  • midbrain7.0 nTPM

Peripheral and autonomic · 16

  • duodenum26.3 nTPM
  • small intestine21.3 nTPM
  • adrenal gland19.4 nTPM
  • colon16.9 nTPM
  • thyroid gland16.2 nTPM
  • liver14.0 nTPM
  • smooth muscle13.9 nTPM
  • lung13.8 nTPM
  • stomach 113.6 nTPM
  • spleen13.1 nTPM
  • urinary bladder12.8 nTPM
  • salivary gland12.8 nTPM
  • kidney11.9 nTPM
  • pancreas11.9 nTPM
  • skeletal muscle10.3 nTPM
  • heart muscle9.3 nTPM

Transcript is not protein. These are RNA levels for KDM4A, shaded on √nTPM so that a three-order range stays legible — on a linear ramp every region but the strongest would read as blank, which looks like absence rather than less. A region carrying no shading is one the atlas reports no consensus value for, not one where the gene is silent. And a gene being transcribed somewhere is not evidence that any compound reaches it. Human Protein Atlas, RNA expression, nTPM (normalized transcripts per million), consensus tissue dataset.

IV · Evidence

Every measurement at this target

Each row links to the ChEMBL assay it came from.

Functional readouts 5

IC₅₀, EC₅₀, AC₅₀ and potency. Assay-dependent, and not interchangeable with a binding constant.

TargetClassTypeValue (nM)pXOrganismAssay
Lysine-specific demethylase 4AEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1737991
Lysine-specific demethylase 4AEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1737991
Lysine-specific demethylase 4AEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1737991
Lysine-specific demethylase 4AEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1737991
Lysine-specific demethylase 4AEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1737991
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