Page last updated: 2024-10-24
regulation of DNA binding
Definition
Target type: biologicalprocess
Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). [GOC:ai, GOC:dph, GOC:tb]
Regulation of DNA binding is a complex and multifaceted process that plays a central role in controlling gene expression. It involves a intricate interplay of various factors, including transcription factors, cofactors, chromatin structure, and environmental cues.
Transcription factors are proteins that bind to specific DNA sequences called regulatory elements, such as promoters and enhancers. These elements can be located near or far from the genes they regulate. Upon binding, transcription factors can either activate or repress gene expression.
The binding of transcription factors to DNA is influenced by several factors:
- **DNA sequence:** Transcription factors have specific DNA-binding domains that recognize and bind to specific nucleotide sequences within regulatory elements.
- **Chromatin structure:** DNA is packaged into chromatin, a complex of DNA and proteins called histones. The accessibility of DNA to transcription factors is influenced by the structure of chromatin. Modifications to histones, such as acetylation and methylation, can alter chromatin structure and regulate gene expression.
- **Cofactors:** Many transcription factors require the assistance of cofactors to bind to DNA or to regulate gene expression. Cofactors can enhance or inhibit the activity of transcription factors.
- **Environmental cues:** Cellular responses to external signals, such as hormones, stress, or nutrient availability, can influence the activity of transcription factors. These signals can trigger signaling pathways that lead to the activation or inactivation of transcription factors.
In addition to transcription factors, other proteins, such as chromatin remodelers and histone modifiers, can also regulate DNA binding. Chromatin remodelers can alter the structure of chromatin, making DNA more or less accessible to transcription factors. Histone modifiers can modify histones, influencing chromatin structure and gene expression.
Regulation of DNA binding is essential for proper cellular function. Dysregulation of this process can contribute to various diseases, including cancer and developmental disorders.'
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Proteins (1)
| Protein | Definition | Taxonomy |
|---|---|---|
| Casein kinase II subunit beta | A casein kinase II subunit beta that is encoded in the genome of human. [PRO:DNx] | Homo sapiens (human) |
Compounds (48)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| 4,5,6,7-tetrabromo-2-azabenzimidazole | 4,5,6,7-tetrabromobenzotriazole: a CK2 kinase inhibitor | ||
| chromone-2-carboxylic acid | chromones | ||
| emodin | emodin : A trihydroxyanthraquinone that is 9,10-anthraquinone which is substituted by hydroxy groups at positions 1, 3, and 8 and by a methyl group at position 6. It is present in the roots and barks of numerous plants (particularly rhubarb and buckthorn), moulds, and lichens. It is an active ingredient of various Chinese herbs. Emodin: Purgative anthraquinone found in several plants, especially RHAMNUS PURSHIANA. It was formerly used as a laxative, but is now used mainly as a tool in toxicity studies. | trihydroxyanthraquinone | antineoplastic agent; laxative; plant metabolite; tyrosine kinase inhibitor |
| n-(2-(methylamino)ethyl)-5-isoquinolinesulfonamide | isoquinolines; sulfonamide | ||
| 2-(4-morpholinyl)-8-phenyl-4h-1-benzopyran-4-one | 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one: specific inhibitor of phosphatidylinositol 3-kinase; structure in first source | chromones; morpholines; organochlorine compound | autophagy inhibitor; EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor; geroprotector |
| mitoxantrone | mitoxantrone : A dihydroxyanthraquinone that is 1,4-dihydroxy-9,10-anthraquinone which is substituted by 6-hydroxy-1,4-diazahexyl groups at positions 5 and 8. Mitoxantrone: An anthracenedione-derived antineoplastic agent. | dihydroxyanthraquinone | analgesic; antineoplastic agent |
| 1,2,5,8-tetrahydroxy anthraquinone | 1,2,5,8-tetrahydroxy anthraquinone: structure in first source quinalizarin : A tetrahydroxyanthraquinone having the four hydroxy groups at the 1-, 2-, 5- and 8-positions. | tetrahydroxyanthraquinone | EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor |
| 3,4-dichlorobenzoic acid | 3,4-dichlorobenzoic acid : A chlorobenzoic acid carrying chloro substituents at positions 3 and 4. 3,4-dichlorobenzoic acid: structure given in first source | chlorobenzoic acid | |
| dichlororibofuranosylbenzimidazole | Dichlororibofuranosylbenzimidazole: An RNA polymerase II transcriptional inhibitor. This compound terminates transcription prematurely by selective inhibition of RNA synthesis. It is used in research to study underlying mechanisms of cellular regulation. | ||
| boldine | aporphine alkaloid | ||
| staurosporine | indolocarbazole alkaloid; organic heterooctacyclic compound | apoptosis inducer; bacterial metabolite; EC 2.7.11.13 (protein kinase C) inhibitor; geroprotector | |
| norharman | beta-carboline : The parent compound of the beta-carbolines, a tricyclic structure comprising an indole ring system ortho- fused to C-3 and C-4 of a pyridine ring. norharman: RN given refers to parent cpd | beta-carbolines; mancude organic heterotricyclic parent | fungal metabolite; marine metabolite |
| 7-n-butyl-6-(4'-hydroxyphenyl)-5h-pyrrolo(2,3b)pyrazine | |||
| purvalanol b | purvalanol B: protein kinase inhibitor; structure in first source | purvalanol | protein kinase inhibitor |
| h 89 | (E)-N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide : A N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide in which the double bond adopts a trans-configuration. N-(2-(4-bromocinnamylamino)ethyl)-5-isoquinolinesulfonamide: structure given in first source N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide : A member of the class of isoquinolines that is the sulfonamide obtained by formal condensation of the sulfo group of isoquinoline-5-sulfonic acid with the primary amino group of N(1)-[3-(4-bromophenyl)prop-2-en-1-yl]ethane-1,2-diamine. It is a protein kinase A inhibitor. | N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide | |
| purvalanol a | 6-((3-chloro)anilino)-2-(isopropyl-2-hydroxyethylamino)-9-isopropylpurine: purvalanol A is the (1R)-isomer; | purvalanol | |
| 4-benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione | 4-benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione: a GSK3beta inhibitor TDZD-8 : A member of the class of thiadiazolidines that is 1,2,4-thiadiazolidine-3,5-dione which is substituted by a methyl group at position 2 and by a benzyl group at position 4. It is a non-ATP competitive inhibitor of glycogen synthase kinase 3beta (GSK3beta). An experimental compound which was being developed for the potential treatment of Alzheimer's disease. | benzenes; thiadiazolidine | anti-inflammatory agent; antineoplastic agent; apoptosis inducer; EC 2.7.11.26 (tau-protein kinase) inhibitor; neuroprotective agent |
| 4,5,6,7-tetrabromobenzimidazole | 4,5,6,7-tetrabromobenzimidazole: structure in first source | ||
| 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 | |
| apigenin | Chamomile: Common name for several daisy-like plants (MATRICARIA; TRIPLEUROSPERMUM; ANTHEMIS; CHAMAEMELUM) native to Europe and Western Asia, now naturalized in the United States and Australia. | trihydroxyflavone | antineoplastic agent; metabolite |
| luteolin | 3'-hydroxyflavonoid; tetrahydroxyflavone | angiogenesis inhibitor; anti-inflammatory agent; antineoplastic agent; apoptosis inducer; c-Jun N-terminal kinase inhibitor; EC 2.3.1.85 (fatty acid synthase) inhibitor; immunomodulator; nephroprotective agent; plant metabolite; radical scavenger; vascular endothelial growth factor receptor antagonist | |
| kaempferol | 7-hydroxyflavonol; flavonols; tetrahydroxyflavone | antibacterial agent; geroprotector; human blood serum metabolite; human urinary metabolite; human xenobiotic metabolite; plant 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 | |
| chrysin | chrysin : A dihydroxyflavone in which the two hydroxy groups are located at positions 5 and 7. | 7-hydroxyflavonol; dihydroxyflavone | anti-inflammatory agent; antineoplastic agent; antioxidant; EC 2.7.11.18 (myosin-light-chain kinase) inhibitor; hepatoprotective agent; plant metabolite |
| fisetin | 3'-hydroxyflavonoid; 7-hydroxyflavonol; tetrahydroxyflavone | anti-inflammatory agent; antioxidant; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; geroprotector; metabolite; plant metabolite | |
| morin | morin : A pentahydroxyflavone that is 7-hydroxyflavonol bearing three additional hydroxy substituents at positions 2' 4' and 5. morin: a light yellowish pigment found in the wood of old fustic (Chlorophora tinctoria) | 7-hydroxyflavonol; pentahydroxyflavone | angiogenesis modulating agent; anti-inflammatory agent; antibacterial agent; antihypertensive agent; antineoplastic agent; antioxidant; EC 5.99.1.2 (DNA topoisomerase) inhibitor; hepatoprotective agent; metabolite; neuroprotective agent |
| myricetin | 7-hydroxyflavonol; hexahydroxyflavone | antineoplastic agent; antioxidant; cyclooxygenase 1 inhibitor; food component; geroprotector; hypoglycemic agent; plant metabolite | |
| coumestrol | coumestrol : A member of the class of coumestans that is coumestan with hydroxy substituents at positions 3 and 9. Coumestrol: A daidzein derivative occurring naturally in forage crops which has some estrogenic activity. | coumestans; delta-lactone; polyphenol | anti-inflammatory agent; antioxidant; plant metabolite |
| ellagic acid | catechols; cyclic ketone; lactone; organic heterotetracyclic compound; polyphenol | antioxidant; EC 1.14.18.1 (tyrosinase) inhibitor; EC 2.3.1.5 (arylamine N-acetyltransferase) inhibitor; EC 2.4.1.1 (glycogen phosphorylase) inhibitor; EC 2.5.1.18 (glutathione transferase) inhibitor; EC 2.7.1.127 (inositol-trisphosphate 3-kinase) inhibitor; EC 2.7.1.151 (inositol-polyphosphate multikinase) inhibitor; EC 2.7.4.6 (nucleoside-diphosphate kinase) inhibitor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; EC 5.99.1.2 (DNA topoisomerase) inhibitor; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; food additive; fungal metabolite; geroprotector; plant metabolite; skin lightening agent | |
| as 605240 | (5Z)-5-(quinoxalin-6-ylmethylidene)-1,3-thiazolidine-2,4-dione : A quinoxaline derivative that is quinoxaline in which the hydrogen at position 6 is replaced by a (2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl group. It is a potent inhibitor of the PI3Kgamma, with an IC50 of 8 nM and inhibits the progression of joint inflammation and damage in both lymphocyte-independent and dependent mouse models of rheumatoid arthritis. 5-quinoxalin-6-ylmethylenethiazolidine-2,4-dione: a PI3Kgamma inhibitor; structure in first source | quinoxaline derivative; thiazolidinediones | anti-inflammatory agent; antirheumatic drug; EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor |
| casein kinase ii | Casein Kinase II: A ubiquitous casein kinase that is comprised of two distinct catalytic subunits and dimeric regulatory subunit. Casein kinase II has been shown to phosphorylate a large number of substrates, many of which are proteins involved in the regulation of gene expression. | ||
| jnj-7706621 | sulfonamide | ||
| pd 184352 | 2-(2-chloro-4-iodophenylamino)-N-cyclopropylmethoxy-3,4-difluorobenzamide: inhibits MAP kinase kinase; structure in first source | aminobenzoic acid | |
| jnj 10198409 | |||
| ps1145 | PS1145: IkappaB kinase inhibitor; structure in first source | beta-carbolines | |
| leucettamine b | leucettamine B: a protein kinase inhibitor isolated from the marine sponge Leucetta microraphis; structure in first source | ||
| danusertib | piperazines | ||
| as 252424 | 5-(5-(4-fluoro-2-hydroxyphenyl)furan-2-ylmethylene)thiazolidine-2,4-dione: a PI3K gamma inhibitor; structure in first source | ||
| 2-({2-[(3-hydroxyphenyl)amino]pyrimidin-4-yl}amino)benzamide | aminopyrimidine; benzamides | protein kinase inhibitor | |
| (e)-3-(2,3,4,5-tetrabromophenyl)acrylic acid | (E)-3-(2,3,4,5-tetrabromophenyl)acrylic acid: casein kinase II inhibitor | ||
| cx 4945 | |||
| entrectinib | entrectinib : A member of the class of indazoles that is 1H-indazole substituted by [4-(4-methylpiperazin-1-yl)-2-(tetrahydro-2H-pyran-4-ylamino)benzoyl]amino and 3,5-difluorobenzyl groups at positions 3 and 5, respectively. It is a potent inhibitor of TRKA, TRKB, TRKC, ROS1, and ALK (IC50 values of 0.1 to 1.7 nM), and used for the treatment of NTRK, ROS1 and ALK gene fusion-positive solid tumours. entrectinib: inhibits TRK, ROS1, and ALK receptor tyrosine kinases; structure in first source | benzamides; difluorobenzene; indazoles; N-methylpiperazine; oxanes; secondary amino compound; secondary carboxamide | antibacterial agent; antineoplastic agent; apoptosis inducer; EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor |
| nms-p118 | NMS-P118: a PARP-1 inhibitor; structure in first source | ||
| cx 5011 | |||
| palinurin | palinurin: an NSAID with antibacterial activity; isolated from Ircinia species; structure in firs t source | ||
| ((5z)5-(1,3-benzodioxol-5-yl)methylene-2-phenylamino-3,5-dihydro-4h-imidazol-4-one) | leucettine L41 : A member of the class of benzodioxoles that is 1,3-benzodioxole substituted by a (2-anilino-5-oxo-1,5-dihydro-4H-imidazol-4-ylidene)methyl group at position 5. It is an inhibitor of DYRK1A, DYRK2, CLK1, and CLK3 (IC50s = 0.04, 0.035, 0.015, and 4.5 muM, respectively). | benzodioxoles; imidazolone; substituted aniline | autophagy inducer; EC 2.7.11.22 (cyclin-dependent kinase) inhibitor; EC 2.7.12.1 (dual-specificity kinase) inhibitor; neuroprotective agent; nootropic agent |
| XL413 | XL413 : A benzofuropyrimidine that is 3,4-dihydro[1]benzofuro[3,2-d]pyrimidine substituted by (2S)-pyrrolidin-2-yl, oxo and chloro groups at positions 2, 4, and 8, respectively. It is a potent ATP competitive inhibitor of Cdc7 kinase (IC50 = 3.4 nM) and exhibits anticancer properties. | benzofuropyrimidine; organochlorine compound; pyrrolidines | antineoplastic agent; EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor |
| nms-e973 | NMS-E973: structure in first source |