Target type: cellularcomponent
A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. [GOC:elh]
The nucleosome is the fundamental repeating unit of chromatin, the complex of DNA and proteins that makes up chromosomes. It consists of a core particle, composed of approximately 147 base pairs of DNA wrapped around a histone octamer, and a linker DNA segment that connects adjacent core particles. The histone octamer comprises two copies of each of the four core histones: H2A, H2B, H3, and H4.
The histone octamer forms a disk-shaped structure with a central channel through which the DNA wraps twice. Each histone has a globular domain that interacts with other histones and a flexible tail domain that extends outwards from the octamer. The histone tails are important for interactions with other proteins and for regulating gene expression.
The DNA wraps around the histone octamer in a left-handed superhelix, with approximately 1.7 turns. The interaction between the DNA and the histones is primarily through electrostatic interactions between the negatively charged DNA backbone and the positively charged amino acid residues of the histones.
The linker DNA segment, which connects adjacent core particles, is typically around 20-80 base pairs in length. It is more accessible to enzymes and other proteins than the DNA wrapped around the histone octamer. The linker DNA length is variable and can be influenced by factors such as the presence of linker histones.
The nucleosome structure is highly dynamic and can undergo various modifications, including post-translational modifications of histones and the addition of histone variants. These modifications can alter the accessibility of DNA to regulatory proteins and influence gene expression.
In summary, the cellular component of a nucleosome consists of a core particle, composed of a histone octamer and 147 base pairs of DNA wrapped around it, and a linker DNA segment connecting adjacent core particles. The histone octamer, composed of two copies of each core histone (H2A, H2B, H3, and H4), is a disk-shaped structure with a central channel through which the DNA wraps twice. The flexible tails of the histones are crucial for interactions with other proteins and gene regulation. The nucleosome structure is dynamic and undergoes modifications that influence gene expression.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| RuvB-like 1 | A RuvB-like 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y265] | Homo sapiens (human) |
| RuvB-like 2 | A RuvB-like 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y230] | Homo sapiens (human) |
| Sphingosine kinase 2 | A sphingosine kinase 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9NRA0] | Homo sapiens (human) |
| Histone acetyltransferase KAT5 | A histone acetyltransferase KAT5 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q92993] | Homo sapiens (human) |
| Lysine-specific histone demethylase 1B | A lysine-specific histone demethylase 2 that is encoded in the genome of human. [PRO:HJD, UniProtKB:Q8NB78] | 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) |
| Protein-glutamine gamma-glutamyltransferase 2 | A protein-glutamine gamma-glutamyltransferase 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P21980] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| 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 |
| 1-(2-naphthalenyl)-3-[(phenylmethyl)-propan-2-ylamino]-1-propanone | ZM39923: structure in first source | naphthalenes | |
| beta-lapachone | beta-lapachone : A benzochromenone that is 3,4-dihydro-2H-benzo[h]chromene-5,6-dione substituted by geminal methyl groups at position 2. Isolated from Tabebuia avellanedae, it exhibits antineoplastic and anti-inflammatory activities. beta-lapachone: antineoplastic inhibitor of reverse transcriptase, DNA topoisomerase, and DNA polymerase | benzochromenone; orthoquinones | anti-inflammatory agent; antineoplastic agent; plant metabolite |
| 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 | |
| vitamin k 3 | Vitamin K 3: A synthetic naphthoquinone without the isoprenoid side chain and biological activity, but can be converted to active vitamin K2, menaquinone, after alkylation in vivo. | 1,4-naphthoquinones; vitamin K | angiogenesis inhibitor; antineoplastic agent; EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitor; human urinary metabolite; nutraceutical |
| 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 |
| 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 | |
| 5-bromoisatin | indoles | anticoronaviral agent | |
| isatin | tribulin: endogenous MONOAMINE OXIDASE inhibitory activity extractable into ethyl acetate found in brain and many mammalian tissues and fluids; ISATIN is a major component; produced in excess following alcohol withdrawal; | indoledione | EC 1.4.3.4 (monoamine oxidase) inhibitor; plant metabolite |
| indirubin | |||
| epigallocatechin gallate | (-)-epigallocatechin 3-gallate : A gallate ester obtained by the formal condensation of gallic acid with the (3R)-hydroxy group of (-)-epigallocatechin. epigallocatechin gallate: a steroid 5alpha-reductase inhibitor and antimutagen in green tea (Camellia sinensis) | flavans; gallate ester; polyphenol | antineoplastic agent; antioxidant; apoptosis inducer; geroprotector; Hsp90 inhibitor; neuroprotective agent; plant metabolite |
| 5-Chloro-1H-indole-2,3-dione | indoles | anticoronaviral agent | |
| coenzyme a | adenosine 3',5'-bisphosphate | coenzyme; Escherichia coli metabolite; mouse metabolite | |
| 5-iodoisatin | 5-iodoisatin: structure in first source | indoles | anticoronaviral agent |
| fingolimod hydrochloride | fingolimod hydrochloride : The hydrochloride salt of 2-amino-2-[2-(4-octylphenyl) ethyl]-1,3-propanediol (fingolimod). Fingolimod Hydrochloride: A sphingosine-derivative and IMMUNOSUPPRESSIVE AGENT that blocks the migration and homing of LYMPHOCYTES to the CENTRAL NERVOUS SYSTEM through its action on SPHINGOSINE 1-PHOSPHATE RECEPTORS. It is used in the treatment of MULTIPLE SCLEROSIS. | hydrochloride | immunosuppressive agent; prodrug; sphingosine-1-phosphate receptor agonist |
| isoindigotin | isoindigotin: used in treatment of chronic granulocytic leukemia; structure given in first source | ||
| anacardic acid | anacardic acid : A hydroxybenzoic acid that is salicylic acid substituted by a pentadecyl group at position 6. It is a major component of cashew nut shell liquid and exhibits an extensive range of bioactivities. anacardic acid: isolated from Anacardium occidentale; monophenol monooxygenase inhibitor | hydroxy monocarboxylic acid; hydroxybenzoic acid | anti-inflammatory agent; antibacterial agent; anticoronaviral agent; apoptosis inducer; EC 2.3.1.48 (histone acetyltransferase) inhibitor; EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitor; neuroprotective agent; plant metabolite |
| sorafenib | (trifluoromethyl)benzenes; aromatic ether; monochlorobenzenes; phenylureas; pyridinecarboxamide | angiogenesis inhibitor; anticoronaviral agent; antineoplastic agent; EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor; ferroptosis inducer; tyrosine kinase inhibitor | |
| n-phenylacrylamide | N-phenylacrylamide: structure in first source | ||
| nsc 95397 | 1,4-naphthoquinones | ||
| ag-213 | tyrphostin 47: inhibits protein-tyrosine kinase activity of EGF-R both in vitro and in living cells; | ||
| 4-(4-(4-chloro-phenyl)thiazol-2-ylamino)phenol | substituted aniline | ||
| (1R,2S)-tranylcypromine hydrochloride | (1R,2S)-tranylcypromine hydrochloride : A hydrochloride obtained by combining (1R,2S)-tranylcypromine with one equivalent of hydrochloric acid. | hydrochloride | |
| sphingosine | 2-aminooctadec-4-ene-1,3-diol : A 2-aminooctadecene-1,3-diol having its double bond at position 4. sphing-4-enine : A sphingenine in which the C=C double bond is located at the 4-position. sphingenine : A 2-aminooctadecene-1,3-diol having (2S,3R)-configuration. sphingoid : Sphinganine, its homologs and stereoisomers, and the hydroxy and unsaturated derivatives of these compounds. | sphing-4-enine | human metabolite; mouse metabolite |
| rottlerin | rottlerin : A chromenol that is 2,2-dimethyl-2H-chromene substituted by hydroxy groups at positions 5 and 7, a 3-acetyl-2,4,6-trihydroxy-5-methylbenzyl group at position 6 and a (1E)-3-oxo-1-phenylprop-1-en-3-yl group at position 8. A potassium channel opener, it is isolated from Mallotus philippensis. rottlerin: an angiogenesis inhibitor; an inhibitor of protein kinase Cdelta (PKCdelta) and calmodulin kinase III; RN refers to (E)-isomer; do not confuse this chalcone with an anthraquinone that is also called rottlerin (RN 481-72-1); | aromatic ketone; benzenetriol; chromenol; enone; methyl ketone | anti-allergic agent; antihypertensive agent; antineoplastic agent; apoptosis inducer; K-ATP channel agonist; metabolite |
| n,n-dimethylsphingenine | N,N-dimethylsphingosine : A sphingoid that is sphingosine in which the two amino hydrogens are replaced by methyl groups. N,N-dimethylsphingosine: a sphingosine kinase inhibitor | aminodiol; sphingoid; tertiary amino compound | EC 2.7.1.91 (sphingosine kinase) inhibitor; metabolite |
| gw-5074 | |||
| 2-hydroxy-6-[(8Z,11Z)-pentadeca-8,11,14-trien-1-yl]benzoic acid | hydroxybenzoic acid | ||
| es-285 | 1-deoxysphinganine : A bioactive sphingoid, sphinganine, in which the terminal hydroxy group has been replaced by a hydrogen. spisulosine: from marine organism, Spisula polynyma; structure in first source | amino alcohol; sphingoid | antineoplastic agent |
| 3-(4-chlorophenyl)-adamantane-1-carboxylic acid (pyridin-4-ylmethyl)amide | organochlorine compound | ||
| bml 258 | |||
| (5-bromo-3-pyridinyl)-[4-(1-pyrrolidinyl)-1-piperidinyl]methanone | aromatic carboxylic acid; pyridinemonocarboxylic acid | ||
| entecavir | benzamides; N-acylpiperidine | ||
| 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 |
| pf-543 | PF-543: Sphingosine Kinase 1 Selective Inhibitor; structure in first source | sulfonamide | |
| rome | (2R)-2-amino-2-(methoxymethyl)-4-(4-octylphenyl)butan-1-ol : A 2-amino-2-(methoxymethyl)-4-(4-octylphenyl)butan-1-ol that has R-configuration. It is a sphingosine kinase-2 inhibitor. Rome: The capital city of Italy. | 2-amino-2-(methoxymethyl)-4-(4-octylphenyl)butan-1-ol | EC 2.7.1.91 (sphingosine kinase) inhibitor |
| 1,2-bis(isothiazol-5-yl)disulfane | 1,2-bis(isothiazol-5-yl)disulfane: structure in first source | ||
| glutaminase | |||
| akt-i-1,2 compound | Akt-I-1,2 compound: an aminopeptidase P inhibitor; structure in first source | ||
| guanylyl imidodiphosphate | guanosine 5'-[beta,gamma-imido]triphosphate : A nucleoside triphosphate analogue that is GTP in which the oxygen atom bridging the beta- to the gamma- phosphate is replaced by a nitrogen atom A non-hydrolyzable analog of GTP, it binds tightly to G-protein in the presence of Mg(2+). Guanylyl Imidodiphosphate: A non-hydrolyzable analog of GTP, in which the oxygen atom bridging the beta to the gamma phosphate is replaced by a nitrogen atom. It binds tightly to G-protein in the presence of Mg2+. The nucleotide is a potent stimulator of ADENYLYL CYCLASES. | nucleoside triphosphate analogue |