Target type: molecularfunction
Binding to a histone in which a residue has been modified by methylation. [GOC:bf, PMID:14585615]
Methylated histone binding is a fundamental molecular process that plays a crucial role in regulating gene expression. It involves the specific interaction between proteins and methylated lysine or arginine residues within histone tails. Histones are the protein components of nucleosomes, the basic structural units of chromatin, which is the complex of DNA and proteins that packages the genome. Methylation of histones is a dynamic process that can be catalyzed by a family of enzymes known as histone methyltransferases (HMTs). These enzymes add methyl groups to specific lysine or arginine residues within histone tails. The pattern of methylation on histone tails can vary depending on the specific residue and the number of methyl groups added. Different methylation patterns are associated with distinct functional outcomes, such as gene activation, silencing, or other regulatory events.
The molecular function of methylated histone binding can be described in terms of its role in modulating chromatin structure and influencing the accessibility of DNA to transcription factors and other regulatory proteins.
* **Chromatin Structure:** Methylated histone binding can directly influence the structure of chromatin. Methylation can induce conformational changes in nucleosomes, which can impact their packing and accessibility. For example, methylation of histone H3 lysine 9 (H3K9) is often associated with the formation of heterochromatin, a densely packed form of chromatin that is generally inactive in gene expression. In contrast, methylation of histone H3 lysine 4 (H3K4) is frequently linked to euchromatin, a more loosely packed form of chromatin that is generally active in gene expression.
* **Transcriptional Regulation:** Methylated histone binding plays a vital role in transcriptional regulation by influencing the recruitment of specific protein complexes to DNA. Different patterns of methylation on histone tails act as "codes" that can be read by specialized "reader" proteins. These reader proteins can be transcription factors, co-activators, or co-repressors that either promote or inhibit gene expression, depending on the specific reader protein involved. For example, the reader protein HP1 binds to methylated H3K9, contributing to heterochromatin formation and transcriptional silencing.
* **DNA Repair:** Methylated histone binding can also be involved in DNA repair pathways. Specific methylation patterns on histone tails can signal the presence of DNA damage and recruit repair proteins to the site of damage, allowing for efficient DNA repair.
Overall, methylated histone binding is a highly complex and dynamic process that is central to the regulation of gene expression and other fundamental cellular processes. The intricate interplay between histone methylation, chromatin structure, and protein recruitment provides a sophisticated system for fine-tuning gene expression in response to various cellular signals and environmental cues.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| Nucleosome-remodeling factor subunit BPTF | A nucleosome-remodeling factor subunit BPTF that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q12830] | Homo sapiens (human) |
| Spindlin-1 | A spindlin-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y657] | Homo sapiens (human) |
| Lethal(3)malignant brain tumor-like protein 1 | A lethal(3)malignant brain tumor-like protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y468] | Homo sapiens (human) |
| Histone lysine demethylase PHF8 | A histone lysine demethylase PHF8 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UPP1] | Homo sapiens (human) |
| Inhibitor of growth protein 2 | An inhibitor of growth protein 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9H160] | Homo sapiens (human) |
| E3 ubiquitin-protein ligase UHRF1 | An E3 ubiquitin-protein ligase UHRF1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96T88] | Homo sapiens (human) |
| Lysine-specific demethylase 7A | A lysine-specific demethylase 7A that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q6ZMT4] | Homo sapiens (human) |
| Polycomb protein SUZ12 | A polycomb protein SUZ12 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15022] | Homo sapiens (human) |
| TP53-binding protein 1 | A TP53-binding protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q12888] | Homo sapiens (human) |
| MBT domain-containing protein 1 | An MBT domain-containing protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q05BQ5] | Homo sapiens (human) |
| WD repeat-containing protein 5 | A WD repeat-containing protein 5 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P61964] | 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) |
| Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7 | A bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P0C870] | Homo sapiens (human) |
| Lysine-specific demethylase 4A | A lysine-specific demethylase 4A that is encoded in the genome of human. [PRO:DNx, UniProtKB:O75164] | Homo sapiens (human) |
| Lysine-specific demethylase PHF2 | A lysine-specific demethylase PHF2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O75151] | Homo sapiens (human) |
| Transcription intermediary factor 1-alpha | A transcription intermediary factor 1-alpha that is encoded in the genome of human. [PRO:DNx, UniProtKB:O15164] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| vanillin | Vanilla: A plant genus of the family ORCHIDACEAE that is the source of the familiar flavoring used in foods and medicines (FLAVORING AGENTS). | benzaldehydes; monomethoxybenzene; phenols | anti-inflammatory agent; anticonvulsant; antioxidant; flavouring agent; plant 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 |
| bifemelane | bifemelane: structure given in first source | diarylmethane | |
| chlorpheniramine | chlorphenamine : A tertiary amino compound that is propylamine which is substituted at position 3 by a pyridin-2-yl group and a p-chlorophenyl group and in which the hydrogens attached to the nitrogen are replaced by methyl groups. A histamine H1 antagonist, it is used to relieve the symptoms of hay fever, rhinitis, urticaria, and asthma. Chlorpheniramine: A histamine H1 antagonist used in allergic reactions, hay fever, rhinitis, urticaria, and asthma. It has also been used in veterinary applications. One of the most widely used of the classical antihistaminics, it generally causes less drowsiness and sedation than PROMETHAZINE. | monochlorobenzenes; pyridines; tertiary amino compound | anti-allergic agent; antidepressant; antipruritic drug; H1-receptor antagonist; histamine antagonist; serotonin uptake inhibitor |
| 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 |
| deferoxamine | Deferoxamine: Natural product isolated from Streptomyces pilosus. It forms iron complexes and is used as a chelating agent, particularly in the mesylate form. desferrioxamine B : An acyclic desferrioxamine that is butanedioic acid in which one of the carboxy groups undergoes formal condensation with the primary amino group of N-(5-aminopentyl)-N-hydroxyacetamide and the second carboxy group undergoes formal condensation with the hydroxyamino group of N(1)-(5-aminopentyl)-N(1)-hydroxy-N(4)-[5-(hydroxyamino)pentyl]butanediamide. It is a siderophore native to Streptomyces pilosus biosynthesised by the DesABCD enzyme cluster as a high affinity Fe(III) chelator. | acyclic desferrioxamine | bacterial metabolite; ferroptosis inhibitor; iron chelator; siderophore |
| 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 | |
| lansoprazole | Lansoprazole: A 2,2,2-trifluoroethoxypyridyl derivative of timoprazole that is used in the therapy of STOMACH ULCERS and ZOLLINGER-ELLISON SYNDROME. The drug inhibits H(+)-K(+)-EXCHANGING ATPASE which is found in GASTRIC PARIETAL CELLS. Lansoprazole is a racemic mixture of (R)- and (S)-isomers. | benzimidazoles; pyridines; sulfoxide | anti-ulcer drug; EC 3.6.3.10 (H(+)/K(+)-exchanging ATPase) inhibitor |
| maprotiline | Maprotiline: A bridged-ring tetracyclic antidepressant that is both mechanistically and functionally similar to the tricyclic antidepressants, including side effects associated with its use. | anthracenes | |
| omeprazole | 5-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl}-1H-benzimidazole : A member of the class of benzimidazoles that is 1H-benzimidazole which is substituted by a [4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl group at position 2 and a methoxy group at position 5. omeprazole : A racemate comprising equimolar amounts of (R)- and (S)-omeprazole. Omeprazole: A 4-methoxy-3,5-dimethylpyridyl, 5-methoxybenzimidazole derivative of timoprazole that is used in the therapy of STOMACH ULCERS and ZOLLINGER-ELLISON SYNDROME. The drug inhibits an H(+)-K(+)-EXCHANGING ATPASE which is found in GASTRIC PARIETAL CELLS. | aromatic ether; benzimidazoles; pyridines; sulfoxide | |
| oxybutynin | oxybutynin : A racemate comprising equimolar amounts of (R)-oxybutynin and esoxybutynin. An antispasmodic used for the treatment of overactive bladder. oxybutynin: RN given refers to parent cpd | acetylenic compound; carboxylic ester; racemate; tertiary alcohol; tertiary amino compound | antispasmodic drug; calcium channel blocker; local anaesthetic; muscarinic antagonist; muscle relaxant; parasympatholytic |
| rabeprazole | Rabeprazole: A 4-(3-methoxypropoxy)-3-methylpyridinyl derivative of timoprazole that is used in the therapy of STOMACH ULCERS and ZOLLINGER-ELLISON SYNDROME. The drug inhibits H(+)-K(+)-EXCHANGING ATPASE which is found in GASTRIC PARIETAL CELLS. | benzimidazoles; pyridines; sulfoxide | anti-ulcer drug; EC 3.6.3.10 (H(+)/K(+)-exchanging ATPase) 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 |
| salicylaldehyde | o-hydroxybenzaldehyde: structure in first source | hydroxybenzaldehyde | nematicide; plant metabolite |
| cyclopentanone | cyclopentanones | Maillard reaction product | |
| 2,4-pyridinedicarboxylic acid | lutidinic acid : A pyridinedicarboxylic acid carrying carboxy groups at positions 2 and 4. | pyridinedicarboxylic acid | |
| cyclooctanone | |||
| daminozide | daminozide: induces tumors | straight-chain fatty acid | |
| toxoflavin | toxoflavin : A pyrimidotriazine that is 1,6-dimethyl-1,5,6,7-tetrahydropyrimido[5,4-e][1,2,4]triazine with oxo groups at positions 5 and 7. toxoflavin: azapteridine antibiotic; structure | carbonyl compound; pyrimidotriazine | antibacterial agent; antineoplastic agent; apoptosis inducer; bacterial metabolite; toxin; virulence factor; Wnt signalling inhibitor |
| 2-hydroxy-4-methoxybenzaldehyde | 2-hydroxy-4-methoxybenzaldehyde: from African medicinal plants: Mondia whitei (Apocynaceae), Rhus vulagaris (Anacardiaceae), Sclerocarya caffra (Anacardiaceae) | methoxybenzenes; phenols | |
| tanshinone | tanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agent | abietane diterpenoid | anticoronaviral agent |
| di-n-desethylamiodarone | di-N-desethylamiodarone: amiodarone metabolite in dogs; structure given in first source | ||
| przewaquinone d | przewaquinone D: isolated from root of Salvia przewalskii; structure given in first source; RN given refers to the trans- isomer, przewaquinone D | ||
| tanshinone ii a | tashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first source | abietane diterpenoid | |
| 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 |
| s-adenosylhomocysteine | S-adenosyl-L-homocysteine : An organic sulfide that is the S-adenosyl derivative of L-homocysteine. S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions. | adenosines; amino acid zwitterion; homocysteine derivative; homocysteines; organic sulfide | cofactor; EC 2.1.1.72 [site-specific DNA-methyltransferase (adenine-specific)] inhibitor; EC 2.1.1.79 (cyclopropane-fatty-acyl-phospholipid synthase) inhibitor; epitope; fundamental metabolite |
| d-2-hydroxyglutarate | (R)-2-hydroxyglutaric acid : The (R)-enantiomer of 2-hydroxyglutaric acid. | 2-hydroxyglutaric acid | algal metabolite |
| alpha-hydroxyglutarate, (l)-isomer | 2-hydroxyglutaric acid | ||
| 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 | ||
| cefsulodin | cefsulodin : A pyridinium-substituted semi-synthetic, broad-spectrum, cephalosporin antibiotic. Cefsulodin: A pyridinium-substituted semisynthetic, broad-spectrum antibacterial used especially for Pseudomonas infections in debilitated patients. | cephalosporin; organosulfonic acid; primary carboxamide | antibacterial drug |
| 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 |
| dexlansoprazole | Dexlansoprazole: The R-isomer of lansoprazole that is used to treat severe GASTROESOPHAGEAL REFLUX DISEASE. | benzimidazoles; sulfoxide | |
| vidofludimus | vidofludimus: a dihydroorotate dehydrogenase inhibitor; structure in first source | ||
| bi 2536 | |||
| au-1 | |||
| unc 0638 | UNC 0638: inhibits lysine methyltransferases G9a and GLP; structure in first source | quinazolines | |
| (5-bromo-3-pyridinyl)-[4-(1-pyrrolidinyl)-1-piperidinyl]methanone | aromatic carboxylic acid; pyridinemonocarboxylic acid | ||
| i-bet726 | |||
| 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 | ||
| epz-6438 | tazemetostat: a histone methyltransferase EZH2 inhibitor with antineoplastic activity | ||
| gsk-2816126 | GSK-2816126: inhibits EZH2 methyltransferase; structure in first source | piperazines; pyridines | |
| gsk343 | GSK343 : A member of the class of indazoles that is 1-isopropyl-1H-indazole-4-carboxamide in which the nitrogen of the carboxamide group is substituted by a (6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl group and in which the indazole ring is substituted at position 6 by a 2-(4-methylpiperazin-1-yl)pyridin-4-yl group. A highly potent and selective EZH2 inhibitor (IC50 = 4 nM). GSK343: an EZH2 methyltransferase inhibitor | aminopyridine; indazoles; N-alkylpiperazine; N-arylpiperazine; pyridone; secondary carboxamide | antineoplastic agent; apoptosis inducer; EC 2.1.1.43 (enhancer of zeste homolog 2) inhibitor |
| oicr-9429 | OICR-9429: antineoplastic; structure in first source | ||
| dBET6 | organic molecular entity |