Target type: molecularfunction
Catalysis of the removal of a methyl group from a tri, a di or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. [PMID:17550896, PMID:22473470]
Histone H3K4me/H3K4me2/H3K4me3 demethylase activity refers to the enzymatic removal of methyl groups from lysine 4 of histone H3, specifically targeting the mono-, di-, and trimethylated states (H3K4me1, H3K4me2, and H3K4me3, respectively). This activity is crucial for regulating gene expression, as methylation at H3K4 is generally associated with active transcription. Demethylation by these enzymes can lead to gene silencing by altering chromatin structure and accessibility to transcription factors. The process involves the oxidation of the methyl group by a dioxygenase enzyme, which converts it to a formaldehyde molecule. This reaction is typically catalyzed by a family of enzymes called lysine-specific demethylases (LSD1/KDM1A) or Jumonji C domain-containing demethylases (JMJD). LSD1 utilizes a flavin adenine dinucleotide (FAD) cofactor and specifically targets mono- and dimethylated H3K4, while JMJD enzymes utilize a non-heme iron and 2-oxoglutarate cofactor and can demethylate all three methylation states of H3K4. The activity of these demethylases is tightly regulated and is often influenced by factors such as cellular signaling pathways, transcription factors, and chromatin modifiers. Dysregulation of H3K4 demethylase activity has been implicated in various diseases, including cancer and developmental disorders.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| 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 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 5B | A lysine-specific demethylase 5B that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UGL1] | Homo sapiens (human) |
| Lysine-specific demethylase 5A | A lysine-specific demethylase 5A that is encoded in the genome of human. [PRO:DNx, UniProtKB:P29375] | 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 |
| 4-hydroxybenzoic acid hydrazide | 4-hydroxybenzohydrazide : A carbohydrazide obtained by formal condensation of the carboxy group of 4-hydroxybenzoic acid with hydrazine. 4-hydroxybenzoic acid hydrazide: metabolite of nifuroxazide | carbohydrazide; phenols | |
| amiodarone | amiodarone : A member of the class of 1-benzofurans that is 1-benzofuran substituted by a butyl group at position 2 and a 4-[2-(diethylamino)ethoxy]-3,5-diiodobenzoyl group at position 3. It is a cardiovascular drug used for the treatment of cardiac dysrhythmias. Amiodarone: An antianginal and class III antiarrhythmic drug. It increases the duration of ventricular and atrial muscle action by inhibiting POTASSIUM CHANNELS and VOLTAGE-GATED SODIUM CHANNELS. There is a resulting decrease in heart rate and in vascular resistance. | 1-benzofurans; aromatic ketone; organoiodine compound; tertiary amino compound | cardiovascular drug |
| 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 |
| disulfiram | organic disulfide; organosulfur acaricide | angiogenesis inhibitor; antineoplastic agent; apoptosis inducer; EC 1.2.1.3 [aldehyde dehydrogenase (NAD(+))] inhibitor; EC 3.1.1.1 (carboxylesterase) inhibitor; EC 3.1.1.8 (cholinesterase) inhibitor; EC 5.99.1.2 (DNA topoisomerase) inhibitor; ferroptosis inducer; fungicide; NF-kappaB 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 |
| 2,4-pyridinedicarboxylic acid | lutidinic acid : A pyridinedicarboxylic acid carrying carboxy groups at positions 2 and 4. | pyridinedicarboxylic acid | |
| daminozide | daminozide: induces tumors | straight-chain fatty acid | |
| di-n-desethylamiodarone | di-N-desethylamiodarone: amiodarone metabolite in dogs; structure given in first source | ||
| deferasirox | deferasirox : A member of the class of triazoles, deferasirox is 1,2,4-triazole substituted by a 4-carboxyphenyl group at position 1 and by 2-hydroxyphenyl groups at positions 3 and 5. An orally active iron chelator, it is used to manage chronic iron overload in patients receiving long-term blood transfusions. Deferasirox: A triazole and benzoate derivative that acts as a selective iron chelator. It is used in the management of chronic IRON OVERLOAD due to blood transfusion or non-transfusion dependent THALASSEMIA. | benzoic acids; monocarboxylic acid; phenols; triazoles | iron chelator |
| 5-carboxy-8-hydroxyquinoline | 5-carboxy-8-hydroxyquinoline: a JmjC histone demethylase inhibitor; structure in first source | quinolines | |
| 6-ethyl-2,5-dimethyl-7-oxo-1H-pyrazolo[1,5-a]pyrimidine-3-carbonitrile | pyrazolopyrimidine | ||
| (1R,2S)-tranylcypromine hydrochloride | (1R,2S)-tranylcypromine hydrochloride : A hydrochloride obtained by combining (1R,2S)-tranylcypromine with one equivalent of hydrochloric acid. | hydrochloride | |
| 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 |
| geldanamycin | 1,4-benzoquinones; ansamycin; carbamate ester; organic heterobicyclic compound | antimicrobial agent; antineoplastic agent; antiviral agent; cysteine protease inhibitor; Hsp90 inhibitor | |
| 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin | 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin: structure in first source alvespimycin : A 19-membered macrocyle that is geldanamycin in which the methoxy group attached to the benzoquinone moiety has been replaced by a 2-(N,N-dimethylamino)ethylamino group. | 1,4-benzoquinones; ansamycin; carbamate ester; secondary amino compound; tertiary amino compound | Hsp90 inhibitor |
| tanespimycin | CP 127374: analog of herbimycin A | 1,4-benzoquinones; ansamycin; carbamate ester; organic heterobicyclic compound; secondary amino compound | antineoplastic agent; apoptosis inducer; Hsp90 inhibitor |
| (5-bromo-3-pyridinyl)-[4-(1-pyrrolidinyl)-1-piperidinyl]methanone | aromatic carboxylic acid; pyridinemonocarboxylic acid | ||
| 3-[[2-(2-pyridinyl)-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)-4-pyrimidinyl]amino]propanoic acid | organonitrogen heterocyclic compound | ||
| entecavir | benzamides; N-acylpiperidine |