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)

ProteinDefinitionTaxonomy
Casein kinase II subunit betaA casein kinase II subunit beta that is encoded in the genome of human. [PRO:DNx]Homo sapiens (human)

Compounds (48)

CompoundDefinitionClassesRoles
4,5,6,7-tetrabromo-2-azabenzimidazole4,5,6,7-tetrabromobenzotriazole: a CK2 kinase inhibitor
chromone-2-carboxylic acidchromones
emodinemodin : 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.
trihydroxyanthraquinoneantineoplastic agent;
laxative;
plant metabolite;
tyrosine kinase inhibitor
n-(2-(methylamino)ethyl)-5-isoquinolinesulfonamideisoquinolines;
sulfonamide
2-(4-morpholinyl)-8-phenyl-4h-1-benzopyran-4-one2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one: specific inhibitor of phosphatidylinositol 3-kinase; structure in first sourcechromones;
morpholines;
organochlorine compound
autophagy inhibitor;
EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor;
geroprotector
mitoxantronemitoxantrone : 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.
dihydroxyanthraquinoneanalgesic;
antineoplastic agent
1,2,5,8-tetrahydroxy anthraquinone1,2,5,8-tetrahydroxy anthraquinone: structure in first source

quinalizarin : A tetrahydroxyanthraquinone having the four hydroxy groups at the 1-, 2-, 5- and 8-positions.
tetrahydroxyanthraquinoneEC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor
3,4-dichlorobenzoic acid3,4-dichlorobenzoic acid : A chlorobenzoic acid carrying chloro substituents at positions 3 and 4.

3,4-dichlorobenzoic acid: structure given in first source
chlorobenzoic acid
dichlororibofuranosylbenzimidazoleDichlororibofuranosylbenzimidazole: 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.
boldineaporphine alkaloid
staurosporineindolocarbazole alkaloid;
organic heterooctacyclic compound
apoptosis inducer;
bacterial metabolite;
EC 2.7.11.13 (protein kinase C) inhibitor;
geroprotector
norharmanbeta-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 bpurvalanol B: protein kinase inhibitor; structure in first sourcepurvalanolprotein 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 a6-((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-dione4-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-tetrabromobenzimidazole4,5,6,7-tetrabromobenzimidazole: structure in first source
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
apigeninChamomile: 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.trihydroxyflavoneantineoplastic agent;
metabolite
luteolin3'-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
kaempferol7-hydroxyflavonol;
flavonols;
tetrahydroxyflavone
antibacterial agent;
geroprotector;
human blood serum metabolite;
human urinary metabolite;
human xenobiotic metabolite;
plant 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
chrysinchrysin : 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
fisetin3'-hydroxyflavonoid;
7-hydroxyflavonol;
tetrahydroxyflavone
anti-inflammatory agent;
antioxidant;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
geroprotector;
metabolite;
plant metabolite
morinmorin : 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
myricetin7-hydroxyflavonol;
hexahydroxyflavone
antineoplastic agent;
antioxidant;
cyclooxygenase 1 inhibitor;
food component;
geroprotector;
hypoglycemic agent;
plant metabolite
coumestrolcoumestrol : 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 acidcatechols;
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 iiCasein 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-7706621sulfonamide
pd 1843522-(2-chloro-4-iodophenylamino)-N-cyclopropylmethoxy-3,4-difluorobenzamide: inhibits MAP kinase kinase; structure in first sourceaminobenzoic acid
jnj 10198409
ps1145PS1145: IkappaB kinase inhibitor; structure in first sourcebeta-carbolines
leucettamine bleucettamine B: a protein kinase inhibitor isolated from the marine sponge Leucetta microraphis; structure in first source
danusertibpiperazines
as 2524245-(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)benzamideaminopyrimidine;
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
entrectinibentrectinib : 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-p118NMS-P118: a PARP-1 inhibitor; structure in first source
cx 5011
palinurinpalinurin: 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
XL413XL413 : 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-e973NMS-E973: structure in first source