Page last updated: 2024-10-24

FAD-dependent H3K4me/H3K4me3 demethylase activity

Definition

Target type: molecularfunction

Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction. [PMID:22473470]

FAD-dependent H3K4me/H3K4me3 demethylase activity refers to the enzymatic process of removing methyl groups from lysine residues at positions 4 and 4 of histone H3, specifically the mono- and tri-methylated forms (H3K4me and H3K4me3). This activity is facilitated by enzymes known as lysine-specific demethylases (LSDs), which use flavin adenine dinucleotide (FAD) as a cofactor.

The removal of methyl groups from H3K4 is crucial for regulating gene expression. H3K4 methylation is generally associated with active transcription, while its demethylation is linked to gene silencing.

Here's a detailed description of the molecular function of FAD-dependent H3K4me/H3K4me3 demethylase activity:

1. **Substrate Recognition and Binding:** LSDs bind to their substrate, the methylated histone H3 tail, via specific recognition domains. These domains typically recognize the histone tail and the specific methylation state of lysine 4.

2. **FAD Cofactor Binding and Oxidation:** FAD, a crucial cofactor, binds to the LSD enzyme. The enzyme then undergoes a conformational change that positions the FAD molecule for oxidation.

3. **Oxygen Activation:** The oxidized FAD molecule facilitates the activation of oxygen, which is required for the demethylation reaction.

4. **Methyl Group Removal:** The activated oxygen molecule then reacts with the methyl group on lysine 4 of H3, leading to its removal as formaldehyde. The FAD cofactor is reduced during this process.

5. **Product Release and Enzyme Regeneration:** After the demethylation reaction, the demethylase releases the demethylated histone H3 and regenerates its FAD cofactor through a series of enzymatic steps.

6. **Gene Expression Regulation:** Demethylation of H3K4 can lead to a decrease in gene expression by reducing the binding affinity of transcription factors and other regulatory proteins to the promoter region.

7. **Cellular Processes:** FAD-dependent H3K4me/H3K4me3 demethylase activity plays a vital role in various cellular processes, including development, cell cycle regulation, and differentiation. Dysregulation of this activity can contribute to various diseases, including cancer.
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Proteins (2)

ProteinDefinitionTaxonomy
Lysine-specific histone demethylase 1BA lysine-specific histone demethylase 2 that is encoded in the genome of human. [PRO:HJD, UniProtKB:Q8NB78]Homo sapiens (human)
Lysine-specific histone demethylase 1AA lysine-specific histone demethylase 1A that is encoded in the genome of human. [PRO:DNx, UniProtKB:O60341]Homo sapiens (human)

Compounds (48)

CompoundDefinitionClassesRoles
berberinealkaloid 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
phenelzinePhenelzine: One of the MONOAMINE OXIDASE INHIBITORS used to treat DEPRESSION; PHOBIC DISORDERS; and PANIC.primary amine
raloxifeneraloxifene : 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
vorinostatvorinostat : 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
2-phenylcyclopropan-1-amine2-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
hesperidinhesperidin : 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
palmatineburasaine: structure in first sourceberberine 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
dehydrocorydalindehydrocorydalin: alkaloid from Corydalis bulbuso D.C. used in therapy of peptic ulcer; RN given refers to parent cpdalkaloid
baicalindihydroxyflavone;
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
hesperetin3'-hydroxyflavanones;
4'-methoxyflavanones;
monomethoxyflavanone;
trihydroxyflavanone
antineoplastic agent;
antioxidant;
plant metabolite
columbamineberberine alkaloid;
organic heterotetracyclic compound
jatrorrhizinejatrorrhizine: isolated from bark of Enantia chlorantha (Annonaceae); structure given in first sourcealkaloid
higenaminehigenamine: structure; RN given refers to (+-)-isomernorcoclaurine
tanshinonetanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agentabietane diterpenoidanticoronaviral agent
cryptotanshinonecryptotanshinone: from Salvia miltiorrhizaabietane diterpenoidanticoronaviral agent
epiberberineepiberberine: isolated in plants of Coptis from China
erlotinibaromatic ether;
quinazolines;
secondary amino compound;
terminal acetylenic compound
antineoplastic agent;
epidermal growth factor receptor antagonist;
protein kinase inhibitor
resveratroltrans-resveratrol : A resveratrol in which the double bond has E configuration.resveratrolantioxidant;
phytoalexin;
plant metabolite;
quorum sensing inhibitor;
radical scavenger
curcumincurcumin : 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
capsaicinALGRX-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.
capsaicinoidnon-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-diaminearomatic ether
mdl 72527MDL 72527: RN given refers to di-HCl; RN for parent cpd not available 6/85; polyamine oxidase inhibitor
wogonosidewogonin 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
quercetin7-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 a4'-methoxyisoflavones;
7-hydroxyisoflavones
antineoplastic agent;
EC 3.5.1.99 (fatty acid amide hydrolase) inhibitor;
phytoestrogen;
plant metabolite;
tyrosine kinase inhibitor
quercetin 3-o-glucopyranosidequercetin 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
rutinHydroxyethylrutoside: Monohydroxyethyl derivative of rutin. Peripheral circulation stimulant used in treatment of venous disorders.disaccharide derivative;
quercetin O-glucoside;
rutinoside;
tetrahydroxyflavone
antioxidant;
metabolite
baicaleintrihydroxyflavoneangiogenesis 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
diosmetin3'-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
diosmindihydroxyflavanone;
disaccharide derivative;
glycosyloxyflavone;
monomethoxyflavone;
rutinoside
anti-inflammatory agent;
antioxidant
mangostinalpha-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
wogoninwogonin : 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 acidgeroprotector;
plant metabolite
afimoxifene
icaritinicaritin: structure in first source
icariinflavonols;
glycosyloxyflavone
antioxidant;
bone density conservation agent;
EC 3.1.4.35 (3',5'-cyclic-GMP phosphodiesterase) inhibitor;
phytoestrogen
baohuoside ibaohuoside I: structure given in first source; isolated from the herb Epimedium davidiiglycosyloxyflavoneanti-inflammatory agent;
antineoplastic agent;
apoptosis inducer;
plant metabolite
salvianolic acid Bsalvianolic 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-glucopyranosideflavonoids;
glycoside
polymyxin b(1)
Dihydrotanshinone Idihydrotanshinone I: extracted from Radix Salviaeabietane diterpenoidanticoronaviral agent
N-(3-ethynylphenyl)-6,7-dimethoxy-4-quinazolinaminequinazolines
1-(4-methyl-1-piperazinyl)-2-[[(1R,2S)-2-(4-phenylmethoxyphenyl)cyclopropyl]amino]ethanoneamino acid amide
gsk2879552GSK2879552 : 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
osimertinibosimertinib : 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