Target type: molecularfunction
Catalysis of the removal of a methyl group from a modified lysine residue at position 4 of the histone H3 protein. [GOC:mah]
Histone H3K4 demethylase activity refers to the enzymatic removal of methyl groups from lysine 4 of histone H3. This activity is critical for regulating gene expression, as methylation of histone H3 at lysine 4 (H3K4me) is generally associated with active transcription. Histone H3K4 demethylases, also known as lysine-specific demethylases (LSDs), play a key role in modulating the epigenetic landscape by removing H3K4 methylation marks. They counteract the activity of histone H3K4 methyltransferases, ensuring a dynamic balance of methylation levels at this crucial residue.
The molecular function of H3K4 demethylases involves a complex interplay of enzymatic activity, protein-protein interactions, and cellular signaling pathways. These enzymes typically possess a catalytic domain that utilizes a unique mechanism to remove methyl groups. This mechanism often involves the oxidation of the methyl group followed by its release as formaldehyde. The catalytic domain is often flanked by other domains that mediate interactions with DNA, other proteins, and regulatory molecules.
H3K4 demethylases are involved in a wide range of cellular processes, including:
* **Transcriptional repression:** By removing activating H3K4me marks, H3K4 demethylases contribute to gene silencing.
* **Cell differentiation:** During development, H3K4 demethylases play a role in switching gene expression patterns, allowing cells to differentiate into specialized cell types.
* **DNA repair:** H3K4 demethylases can regulate the accessibility of damaged DNA to repair machinery.
* **Immune response:** H3K4 demethylases are implicated in the regulation of immune cell function and inflammatory responses.
* **Disease pathogenesis:** Dysregulation of H3K4 demethylase activity has been linked to various diseases, including cancer, neurodevelopmental disorders, and autoimmune diseases.
Understanding the molecular function of H3K4 demethylases is crucial for comprehending the intricate mechanisms that govern gene expression and cellular processes. Their role in regulating epigenetic landscapes and their involvement in diverse biological pathways make them important targets for therapeutic interventions in various diseases.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| Lysine-specific demethylase 5B | A lysine-specific demethylase 5B that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UGL1] | Homo sapiens (human) |
| Lysine-specific demethylase 5D | A lysine-specific demethylase 5D that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9BY66] | Homo sapiens (human) |
| Lysine-specific demethylase 5C | A lysine-specific demethylase 5C that is encoded in the genome of human. [PRO:DNx, UniProtKB:P41229] | Homo sapiens (human) |
| Lysine-specific histone demethylase 1A | A lysine-specific histone demethylase 1A that is encoded in the genome of human. [PRO:DNx, UniProtKB:O60341] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| alpha-ketoglutaric acid | 2-oxoglutaric acid : An oxo dicarboxylic acid that consists of glutaric acid bearing an oxo substituent at position 2. It is an intermediate metabolite in Krebs cycle. | oxo dicarboxylic acid | fundamental metabolite |
| berberine | alkaloid antibiotic; berberine alkaloid; botanical anti-fungal agent; organic heteropentacyclic compound | antilipemic drug; antineoplastic agent; antioxidant; EC 1.1.1.141 [15-hydroxyprostaglandin dehydrogenase (NAD(+))] inhibitor; EC 1.1.1.21 (aldehyde reductase) inhibitor; EC 1.13.11.52 (indoleamine 2,3-dioxygenase) inhibitor; EC 1.21.3.3 (reticuline oxidase) inhibitor; EC 2.1.1.116 [3'-hydroxy-N-methyl-(S)-coclaurine 4'-O-methyltransferase] inhibitor; EC 2.1.1.122 [(S)-tetrahydroprotoberberine N-methyltransferase] inhibitor; EC 2.7.11.10 (IkappaB kinase) inhibitor; EC 3.1.1.4 (phospholipase A2) inhibitor; EC 3.1.1.7 (acetylcholinesterase) inhibitor; EC 3.1.1.8 (cholinesterase) inhibitor; EC 3.1.3.48 (protein-tyrosine-phosphatase) inhibitor; EC 3.4.14.5 (dipeptidyl-peptidase IV) inhibitor; EC 3.4.21.26 (prolyl oligopeptidase) inhibitor; geroprotector; hypoglycemic agent; metabolite; potassium channel blocker | |
| deferiprone | deferiprone : A member of the class of 4-pyridones that is pyridin-4(1H)-one substituted at positions 1 and 2 by methyl groups and at position 3 by a hydroxy group. A lipid-soluble iron-chelator used for treatment of thalassaemia. Deferiprone: A pyridone derivative and iron chelator that is used in the treatment of IRON OVERLOAD in patients with THALASSEMIA. | 4-pyridones | iron chelator; protective agent |
| phenelzine | Phenelzine: One of the MONOAMINE OXIDASE INHIBITORS used to treat DEPRESSION; PHOBIC DISORDERS; and PANIC. | primary amine | |
| raloxifene | raloxifene : A member of the class of 1-benzothiophenes that is 1-benzothiophene in which the hydrogens at positions 2, 3, and 6 have been replaced by p-hydroxyphenyl, p-[2-(piperidin-1-yl)ethoxy]benzoyl, and hydroxy groups, respectively. | 1-benzothiophenes; aromatic ketone; N-oxyethylpiperidine; phenols | bone density conservation agent; estrogen antagonist; estrogen receptor modulator |
| vorinostat | vorinostat : A dicarboxylic acid diamide comprising suberic (octanedioic) acid coupled to aniline and hydroxylamine. A histone deacetylase inhibitor, it is marketed under the name Zolinza for the treatment of cutaneous T cell lymphoma (CTCL). Vorinostat: A hydroxamic acid and anilide derivative that acts as a HISTONE DEACETYLASE inhibitor. It is used in the treatment of CUTANEOUS T-CELL LYMPHOMA and SEZARY SYNDROME. | dicarboxylic acid diamide; hydroxamic acid | antineoplastic agent; apoptosis inducer; EC 3.5.1.98 (histone deacetylase) inhibitor |
| succinylacetone | 4,6-dioxoheptanoic acid : A dioxo monocarboxylic acid that is heptanoic acid in which oxo groups replace the hydrogens at positions 4 and 6. It is an abnormal metabolite of the tyrosine metabolic pathway and a marker for type 1 tyrosinaemia. succinylacetone: inhibitor of heme biosynthesis | beta-diketone; dioxo monocarboxylic acid | human metabolite |
| 2-phenylcyclopropan-1-amine | 2-phenylcyclopropan-1-amine : A member of the class of cyclopropanes carrying amino and phenyl substituents at positions 1 and 2 respectively. | benzenes; cyclopropanes; primary amine | |
| 2,4-pyridinedicarboxylic acid | lutidinic acid : A pyridinedicarboxylic acid carrying carboxy groups at positions 2 and 4. | pyridinedicarboxylic acid | |
| hesperidin | hesperidin : A disaccharide derivative that consists of hesperetin substituted by a 6-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyl moiety at position 7 via a glycosidic linkage. Hesperidin: A flavanone glycoside found in CITRUS fruit peels. | 3'-hydroxyflavanones; 4'-methoxyflavanones; dihydroxyflavanone; disaccharide derivative; flavanone glycoside; monomethoxyflavanone; rutinoside | mutagen |
| daminozide | daminozide: induces tumors | straight-chain fatty acid | |
| palmatine | burasaine: structure in first source | berberine alkaloid; organic heterotetracyclic compound | plant metabolite |
| tranylcypromine | (1R,2S)-tranylcypromine : A 2-phenylcyclopropan-1-amine that is the (1R,2S)-enantiomer of tranylcypromine. tranylcypromine : A racemate comprising equal amounts of (1R,2S)- and (1S,2R)-2-phenylcyclopropan-1-amine. An irreversible monoamine oxidase inhibitor that is used as an antidepressant (INN tranylcypromine). Tranylcypromine: A propylamine formed from the cyclization of the side chain of amphetamine. This monoamine oxidase inhibitor is effective in the treatment of major depression, dysthymic disorder, and atypical depression. It also is useful in panic and phobic disorders. (From AMA Drug Evaluations Annual, 1994, p311) | 2-phenylcyclopropan-1-amine | |
| (1S,2R)-tranylcypromine | (1S,2R)-tranylcypromine : A 2-phenylcyclopropan-1-amine that is the (1S,2R)-enantiomer of tranylcypromine. | 2-phenylcyclopropan-1-amine | |
| dehydrocorydalin | dehydrocorydalin: alkaloid from Corydalis bulbuso D.C. used in therapy of peptic ulcer; RN given refers to parent cpd | alkaloid | |
| baicalin | dihydroxyflavone; glucosiduronic acid; glycosyloxyflavone; monosaccharide derivative | antiatherosclerotic agent; antibacterial agent; anticoronaviral agent; antineoplastic agent; antioxidant; cardioprotective agent; EC 2.7.7.48 (RNA-directed RNA polymerase) inhibitor; EC 3.4.21.26 (prolyl oligopeptidase) inhibitor; ferroptosis inhibitor; neuroprotective agent; non-steroidal anti-inflammatory drug; plant metabolite; prodrug | |
| hesperetin | 3'-hydroxyflavanones; 4'-methoxyflavanones; monomethoxyflavanone; trihydroxyflavanone | antineoplastic agent; antioxidant; plant metabolite | |
| columbamine | berberine alkaloid; organic heterotetracyclic compound | ||
| jatrorrhizine | jatrorrhizine: isolated from bark of Enantia chlorantha (Annonaceae); structure given in first source | alkaloid | |
| higenamine | higenamine: structure; RN given refers to (+-)-isomer | norcoclaurine | |
| tanshinone | tanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agent | abietane diterpenoid | anticoronaviral agent |
| cryptotanshinone | cryptotanshinone: from Salvia miltiorrhiza | abietane diterpenoid | anticoronaviral agent |
| epiberberine | epiberberine: isolated in plants of Coptis from China | ||
| erlotinib | aromatic ether; quinazolines; secondary amino compound; terminal acetylenic compound | antineoplastic agent; epidermal growth factor receptor antagonist; protein kinase inhibitor | |
| resveratrol | trans-resveratrol : A resveratrol in which the double bond has E configuration. | resveratrol | antioxidant; phytoalexin; plant metabolite; quorum sensing inhibitor; radical scavenger |
| 5-carboxy-8-hydroxyquinoline | 5-carboxy-8-hydroxyquinoline: a JmjC histone demethylase inhibitor; structure in first source | quinolines | |
| curcumin | curcumin : A beta-diketone that is methane in which two of the hydrogens are substituted by feruloyl groups. A natural dyestuff found in the root of Curcuma longa. Curcumin: A yellow-orange dye obtained from tumeric, the powdered root of CURCUMA longa. It is used in the preparation of curcuma paper and the detection of boron. Curcumin appears to possess a spectrum of pharmacological properties, due primarily to its inhibitory effects on metabolic enzymes. | aromatic ether; beta-diketone; diarylheptanoid; enone; polyphenol | anti-inflammatory agent; antifungal agent; antineoplastic agent; biological pigment; contraceptive drug; dye; EC 1.1.1.205 (IMP dehydrogenase) inhibitor; EC 1.1.1.21 (aldehyde reductase) inhibitor; EC 1.1.1.25 (shikimate dehydrogenase) inhibitor; EC 1.6.5.2 [NAD(P)H dehydrogenase (quinone)] inhibitor; EC 1.8.1.9 (thioredoxin reductase) inhibitor; EC 2.7.10.2 (non-specific protein-tyrosine kinase) inhibitor; EC 3.5.1.98 (histone deacetylase) inhibitor; flavouring agent; food colouring; geroprotector; hepatoprotective agent; immunomodulator; iron chelator; ligand; lipoxygenase inhibitor; metabolite; neuroprotective agent; nutraceutical; radical scavenger |
| capsaicin | ALGRX-4975: an injectable capsaicin (TRPV1 receptor agonist) formulation for longlasting pain relief capsaicinoid : A family of aromatic fatty amides produced as secondary metabolites by chilli peppers. | capsaicinoid | non-narcotic analgesic; TRPV1 agonist; voltage-gated sodium channel blocker |
| (1R,2S)-tranylcypromine hydrochloride | (1R,2S)-tranylcypromine hydrochloride : A hydrochloride obtained by combining (1R,2S)-tranylcypromine with one equivalent of hydrochloric acid. | hydrochloride | |
| N5-(2-chloro-6-phenoxybenzyl)-1H-1,2,4-triazole-3,5-diamine | aromatic ether | ||
| mdl 72527 | MDL 72527: RN given refers to di-HCl; RN for parent cpd not available 6/85; polyamine oxidase inhibitor | ||
| oxalylglycine | N-oxalylglycine : An amino dicarboxylic acid that is iminodiacetic acid with an oxo substituent. It is used as an inhibitor of alpha-ketoglutarate dependent (EC 1.14.11.*) enzymes. oxalylglycine: structure given in first source | amino dicarboxylic acid; N-acylglycine | EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitor |
| wogonoside | wogonin 7-O-beta-D-glucuronide : The glycosyloxyflavone which is the 7-O-glucuronide of wogonin. wogonoside: from Scutellaria baicalensis; structure in first source | beta-D-glucosiduronic acid; glycosyloxyflavone; monohydroxyflavone; monomethoxyflavone; monosaccharide derivative | |
| quercetin | 7-hydroxyflavonol; pentahydroxyflavone | antibacterial agent; antineoplastic agent; antioxidant; Aurora kinase inhibitor; chelator; EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor; geroprotector; phytoestrogen; plant metabolite; protein kinase inhibitor; radical scavenger | |
| biochanin a | 4'-methoxyisoflavones; 7-hydroxyisoflavones | antineoplastic agent; EC 3.5.1.99 (fatty acid amide hydrolase) inhibitor; phytoestrogen; plant metabolite; tyrosine kinase inhibitor | |
| quercetin 3-o-glucopyranoside | quercetin 3-O-beta-D-glucopyranoside : A quercetin O-glucoside that is quercetin with a beta-D-glucosyl residue attached at position 3. Isolated from Lepisorus contortus, it exhibits antineoplastic activityand has been found to decrease the rate of polymerization and sickling of red blood cells quercetin 3-O-glucopyranoside: structure in first source | beta-D-glucoside; monosaccharide derivative; quercetin O-glucoside; tetrahydroxyflavone | antineoplastic agent; antioxidant; antipruritic drug; bone density conservation agent; geroprotector; histamine antagonist; osteogenesis regulator; plant metabolite |
| rutin | Hydroxyethylrutoside: Monohydroxyethyl derivative of rutin. Peripheral circulation stimulant used in treatment of venous disorders. | disaccharide derivative; quercetin O-glucoside; rutinoside; tetrahydroxyflavone | antioxidant; metabolite |
| baicalein | trihydroxyflavone | angiogenesis inhibitor; anti-inflammatory agent; antibacterial agent; anticoronaviral agent; antifungal agent; antineoplastic agent; antioxidant; apoptosis inducer; EC 1.13.11.31 (arachidonate 12-lipoxygenase) inhibitor; EC 1.13.11.33 (arachidonate 15-lipoxygenase) inhibitor; EC 3.4.21.26 (prolyl oligopeptidase) inhibitor; EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitor; EC 4.1.1.17 (ornithine decarboxylase) inhibitor; ferroptosis inhibitor; geroprotector; hormone antagonist; plant metabolite; prostaglandin antagonist; radical scavenger | |
| diosmetin | 3'-hydroxyflavonoid; monomethoxyflavone; trihydroxyflavone | angiogenesis inhibitor; anti-inflammatory agent; antineoplastic agent; antioxidant; apoptosis inducer; bone density conservation agent; cardioprotective agent; plant metabolite; tropomyosin-related kinase B receptor agonist; vasodilator agent | |
| diosmin | dihydroxyflavanone; disaccharide derivative; glycosyloxyflavone; monomethoxyflavone; rutinoside | anti-inflammatory agent; antioxidant | |
| mangostin | alpha-mangostin : A member of the class of xanthones that is 9H-xanthene substituted by hydroxy group at positions 1, 3 and 6, a methoxy group at position 7, an oxo group at position 9 and prenyl groups at positions 2 and 8. Isolated from the stems of Cratoxylum cochinchinense, it exhibits antioxidant, antimicrobial and antitumour activities. mangostin: xanthone from rind of Garcinia mangostana Linn. fruit | aromatic ether; phenols; xanthones | antimicrobial agent; antineoplastic agent; antioxidant; plant metabolite |
| wogonin | wogonin : A dihydroxy- and monomethoxy-flavone in which the hydroxy groups are positioned at C-5 and C-7 and the methoxy group is at C-8. wogonin: structure in first source | dihydroxyflavone; monomethoxyflavone | angiogenesis inhibitor; antineoplastic agent; cyclooxygenase 2 inhibitor; plant metabolite |
| rosmarinic acid | (R)-rosmarinic acid : A stereoisomer of rosmarinic acid having (R)-configuration. rosmarinic acid : The 1-carboxy-2-(2,4-dihydroxyphenyl)ethyl ester of trans-caffeic acid. rosmarinic acid: RN given refers to parent cpd; promote OT project | rosmarinic acid | geroprotector; plant metabolite |
| afimoxifene | |||
| icaritin | icaritin: structure in first source | ||
| icariin | flavonols; glycosyloxyflavone | antioxidant; bone density conservation agent; EC 3.1.4.35 (3',5'-cyclic-GMP phosphodiesterase) inhibitor; phytoestrogen | |
| baohuoside i | baohuoside I: structure given in first source; isolated from the herb Epimedium davidii | glycosyloxyflavone | anti-inflammatory agent; antineoplastic agent; apoptosis inducer; plant metabolite |
| salvianolic acid B | salvianolic acid B : A member of the class of 1-benzofurans that is an antioxidant and free radical scavenging compound extracted from S. miltiorrhiza salvianolic acid B: isolated from Salvia miltiorrhiza | 1-benzofurans; catechols; dicarboxylic acid; enoate ester; polyphenol | anti-inflammatory agent; antidepressant; antineoplastic agent; antioxidant; apoptosis inducer; autophagy inhibitor; cardioprotective agent; hepatoprotective agent; hypoglycemic agent; neuroprotective agent; osteogenesis regulator; plant metabolite |
| Diosmetin 7-O-beta-D-glucopyranoside | flavonoids; glycoside | ||
| polymyxin b(1) | |||
| Dihydrotanshinone I | dihydrotanshinone I: extracted from Radix Salviae | abietane diterpenoid | anticoronaviral agent |
| N-(3-ethynylphenyl)-6,7-dimethoxy-4-quinazolinamine | quinazolines | ||
| 1-(4-methyl-1-piperazinyl)-2-[[(1R,2S)-2-(4-phenylmethoxyphenyl)cyclopropyl]amino]ethanone | amino acid amide | ||
| 3-[[2-(2-pyridinyl)-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)-4-pyrimidinyl]amino]propanoic acid | organonitrogen heterocyclic compound | ||
| gsk2879552 | GSK2879552 : A member of the class of piperidines that is piperidine substituted by (4-carboxyphenyl)methyl and {[(1R,2S)-2-phenylcyclopropyl]amino}methyl groups at positions 1 and 4, respectively. It is a potent and irreversible inhibitor of lysine specific demethylase 1 (LSD1, also known as KDM1A). It was under clinical investigation for the treatment of acute myeloid leukaemia and small cell lung carcinoma. GSK2879552: inhibits lysine demethylase 1; structure in first source | benzenes; benzoic acids; cyclopropanes; monocarboxylic acid; piperidines; secondary amino compound; tertiary amino compound | antineoplastic agent; EC 1.14.99.66 (lysine-specific histone demethylase 1A) inhibitor |
| osimertinib | osimertinib : A member of the class of aminopyrimidines that is 4-(1-methylindol-3-yl)pyrimidin-2-amine in which one of the amino hydrogens is replaced by a 2-methoxy-4-[2-(dimethylamino)ethyl](methyl)amino-5-acrylamidophenyl group. Used (as the mesylate salt) for treatment of EGFR T790M mutation positive non-small cell lung cancer. osimertinib: an EGFR tyrosine kinase inhibitor | acrylamides; aminopyrimidine; biaryl; indoles; monomethoxybenzene; secondary amino compound; secondary carboxamide; substituted aniline; tertiary amino compound | antineoplastic agent; epidermal growth factor receptor antagonist |