Target type: molecularfunction
Binding to messenger RNA (mRNA) of a specific nucleotide composition or a specific sequence motif. [PMID:11886857]
Sequence-specific mRNA binding is a fundamental process in gene expression, playing a critical role in regulating the fate of mRNA molecules. This molecular function involves proteins, often referred to as RNA-binding proteins (RBPs), that specifically recognize and bind to short sequences within mRNA molecules. These sequences, known as RNA recognition motifs (RRMs), can be as short as 4-6 nucleotides and are often located within the 5' untranslated region (UTR), 3' UTR, or coding sequence of the mRNA. The recognition and binding of RBPs to their cognate sequences can trigger a cascade of downstream events, including:
1. **Translation regulation:** RBPs can influence the initiation, elongation, or termination of translation, thereby controlling the rate at which a particular mRNA is translated into protein.
2. **mRNA stability:** Some RBPs act as protectors, stabilizing mRNA molecules and preventing their degradation. Others can act as destabilizers, marking mRNAs for degradation.
3. **mRNA localization:** RBPs can direct mRNAs to specific subcellular compartments, where they are needed for localized protein synthesis.
4. **Splicing regulation:** RBPs can influence the splicing process, affecting which exons are included or excluded from a mature mRNA molecule.
5. **Post-transcriptional modification:** RBPs can recruit enzymes that modify mRNAs, such as methylation or adenylation, affecting their stability or translation efficiency.
The intricate interplay between RBPs and their target mRNAs is essential for maintaining cellular homeostasis, responding to environmental cues, and regulating developmental processes. Dysregulation of mRNA binding often leads to disease, highlighting the importance of understanding this complex molecular function.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| Thymidylate synthase | A thymidylate synthase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P04818] | Homo sapiens (human) |
| Dihydrofolate reductase | A dihydrofolate reductase that is encoded in the genome of human. [PRO:DAN, UniProtKB:P00374] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| hippuric acid | hippuric acid: RN given refers to parent cpd; structure in Merck Index, 9th ed, #4591 N-benzoylglycine : An N-acylglycine in which the acyl group is specified as benzoyl. | N-acylglycine | human blood serum metabolite; uremic toxin |
| ag 1295 | quinoxaline derivative | geroprotector | |
| diclofenac | diclofenac : A monocarboxylic acid consisting of phenylacetic acid having a (2,6-dichlorophenyl)amino group at the 2-position. Diclofenac: A non-steroidal anti-inflammatory agent (NSAID) with antipyretic and analgesic actions. It is primarily available as the sodium salt. | amino acid; aromatic amine; dichlorobenzene; monocarboxylic acid; secondary amino compound | antipyretic; drug allergen; EC 1.14.99.1 (prostaglandin-endoperoxide synthase) inhibitor; environmental contaminant; non-narcotic analgesic; non-steroidal anti-inflammatory drug; xenobiotic |
| diflunisal | diflunisal : An organofluorine compound comprising salicylic acid having a 2,4-difluorophenyl group at the 5-position. Diflunisal: A salicylate derivative and anti-inflammatory analgesic with actions and side effects similar to those of ASPIRIN. | monohydroxybenzoic acid; organofluorine compound | non-narcotic analgesic; non-steroidal anti-inflammatory drug |
| etodolac | etodolac : A monocarboxylic acid that is acetic acid in which one of the methyl hydrogens is substituted by a 1,8-diethyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl moiety. A preferential inhibitor of cyclo-oxygenase 2 and non-steroidal anti-inflammatory, it is used for the treatment of rheumatoid arthritis and osteoarthritis, and for the alleviation of postoperative pain. Administered as the racemate, only the (S)-enantiomer is active. Etodolac: A non-steroidal anti-inflammatory agent and cyclooxygenase-2 (COX-2) inhibitor with potent analgesic and anti-arthritic properties. It has been shown to be effective in the treatment of OSTEOARTHRITIS; RHEUMATOID ARTHRITIS; ANKYLOSING SPONDYLITIS; and in the alleviation of postoperative pain (PAIN, POSTOPERATIVE). | monocarboxylic acid; organic heterotricyclic compound | antipyretic; cyclooxygenase 2 inhibitor; non-narcotic analgesic; non-steroidal anti-inflammatory drug |
| fenbufen | fenbufen: structure; RN given refers to parent cpd | 4-oxo monocarboxylic acid; biphenyls | non-steroidal anti-inflammatory drug |
| ibuprofen | Midol: combination of cinnamedrine, phenacetin, aspirin & caffeine | monocarboxylic acid | antipyretic; cyclooxygenase 1 inhibitor; cyclooxygenase 2 inhibitor; drug allergen; environmental contaminant; geroprotector; non-narcotic analgesic; non-steroidal anti-inflammatory drug; radical scavenger; xenobiotic |
| mefenamic acid | mefenamic acid : An aminobenzoic acid that is anthranilic acid in which one of the hydrogens attached to the nitrogen is replaced by a 2,3-dimethylphenyl group. Although classed as a non-steroidal anti-inflammatory drug, its anti-inflammatory properties are considered to be minor. It is used to relieve mild to moderate pain, including headaches, dental pain, osteoarthritis and rheumatoid arthritis. Mefenamic Acid: A non-steroidal anti-inflammatory agent with analgesic, anti-inflammatory, and antipyretic properties. It is an inhibitor of cyclooxygenase. | aminobenzoic acid; secondary amino compound | analgesic; antipyretic; antirheumatic drug; EC 1.14.99.1 (prostaglandin-endoperoxide synthase) inhibitor; environmental contaminant; non-steroidal anti-inflammatory drug; xenobiotic |
| metformin | metformin : A member of the class of guanidines that is biguanide the carrying two methyl substituents at position 1. Metformin: A biguanide hypoglycemic agent used in the treatment of non-insulin-dependent diabetes mellitus not responding to dietary modification. Metformin improves glycemic control by improving insulin sensitivity and decreasing intestinal absorption of glucose. (From Martindale, The Extra Pharmacopoeia, 30th ed, p289) | guanidines | environmental contaminant; geroprotector; hypoglycemic agent; xenobiotic |
| doxorubicin hydrochloride | folic acids | ||
| pd 153035 | 4-((3-bromophenyl)amino)-6,7-dimethoxyquinazoline: structure given in first source PD-153035 : A member of the class of quinazolines carrying a 3-bromophenylamino substituent at position 4 and two methoxy substituents at positions 6 and 7. | aromatic amine; aromatic ether; bromobenzenes; quinazolines; secondary amino compound | EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor; epidermal growth factor receptor antagonist |
| phenolphthalein | Phenolphthalein: An acid-base indicator which is colorless in acid solution, but turns pink to red as the solution becomes alkaline. It is used medicinally as a cathartic. | phenols | |
| pyrimethamine | Maloprim: contains above 2 cpds | aminopyrimidine; monochlorobenzenes | antimalarial; antiprotozoal drug; EC 1.5.1.3 (dihydrofolate reductase) inhibitor |
| riluzole | Riluzole: A glutamate antagonist (RECEPTORS, GLUTAMATE) used as an anticonvulsant (ANTICONVULSANTS) and to prolong the survival of patients with AMYOTROPHIC LATERAL SCLEROSIS. | benzothiazoles | |
| sulfacetamide | sulfacetamide : A sulfonamide that is sulfanilamide acylated on the sulfonamide nitrogen. Sulfacetamide: An anti-bacterial agent that is used topically to treat skin infections and orally for urinary tract infections. | N-sulfonylcarboxamide; substituted aniline | antibacterial drug; antiinfective agent; antimicrobial agent; EC 2.5.1.15 (dihydropteroate synthase) inhibitor |
| trimethoprim | trimethoprim : An aminopyrimidine antibiotic whose structure consists of pyrimidine 2,4-diamine and 1,2,3-trimethoxybenzene moieties linked by a methylene bridge. Trimethoprim: A pyrimidine inhibitor of dihydrofolate reductase, it is an antibacterial related to PYRIMETHAMINE. It is potentiated by SULFONAMIDES and the TRIMETHOPRIM, SULFAMETHOXAZOLE DRUG COMBINATION is the form most often used. It is sometimes used alone as an antimalarial. TRIMETHOPRIM RESISTANCE has been reported. | aminopyrimidine; methoxybenzenes | antibacterial drug; diuretic; drug allergen; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; environmental contaminant; xenobiotic |
| trimetrexate | Trimetrexate: A nonclassical folic acid inhibitor through its inhibition of the enzyme dihydrofolate reductase. It is being tested for efficacy as an antineoplastic agent and as an antiparasitic agent against PNEUMOCYSTIS PNEUMONIA in AIDS patients. Myelosuppression is its dose-limiting toxic effect. | ||
| tryptophan | tryptophan : An alpha-amino acid that is alanine bearing an indol-3-yl substituent at position 3. Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals. | erythrose 4-phosphate/phosphoenolpyruvate family amino acid; L-alpha-amino acid; L-alpha-amino acid zwitterion; proteinogenic amino acid; tryptophan; tryptophan zwitterion | antidepressant; Escherichia coli metabolite; human metabolite; micronutrient; mouse metabolite; nutraceutical; plant metabolite; Saccharomyces cerevisiae metabolite |
| 1,8-naphthalenedicarboxylic acid anhydride | 1,8-naphthalenedicarboxylic acid anhydride: used as seed protector from herbicides | cyclic dicarboxylic anhydride | |
| phenformin | phenformin : A member of the class of biguanides that is biguanide in which one of the terminal nitrogen atoms is substituted by a 2-phenylethyl group. It was used as an anti-diabetic drug but was later withdrawn from the market due to potential risk of lactic acidosis. Phenformin: A biguanide hypoglycemic agent with actions and uses similar to those of METFORMIN. Although it is generally considered to be associated with an unacceptably high incidence of lactic acidosis, often fatal, it is still available in some countries. (From Martindale, The Extra Pharmacopoeia, 30th ed, p290) | biguanides | antineoplastic agent; geroprotector; hypoglycemic agent |
| fluorodeoxyuridylate | Fluorodeoxyuridylate: 5-Fluoro-2'-deoxyuridylate. An inhibitor of thymidylate synthetase. Formed from 5-fluorouracil or 5-fluorodeoxyuridine. | pyrimidine 2'-deoxyribonucleoside 5'-monophosphate | |
| cycloguanil | cycloguanil : A triazine in which a 1,6-dihydro-1,3,5-triazine ring is substituted at N-1 by a 4-chlorophenyl group, at C-2 and -4 by amino groups and at C-6 by gem-dimethyl groups. A dihydrofolate reductase inhibitor, it is a metabolite of the antimalarial drug proguanil. cycloguanil: the active metabolite of proguanil; antifolate drug; structure in first source | triazines | antifolate; antiinfective agent; antimalarial; antiparasitic agent; antiprotozoal drug; EC 1.5.1.3 (dihydrofolate reductase) inhibitor |
| D-tryptophan | D-alpha-amino acid; tryptophan; tryptophan zwitterion | bacterial metabolite | |
| congo red | Congo Red : An indicator dye that is blue-violet at pH 3.0 and red at pH 5.0. Congo Red: An acid dye used in testing for hydrochloric acid in gastric contents. It is also used histologically to test for AMYLOIDOSIS. | bis(azo) compound | |
| 4,6-diamino-2,2-dimethyl-1,2-dihydro-1-phenyl-s-triazine | 4,6-diamino-2,2-dimethyl-1,2-dihydro-1-phenyl-s-triazine: structure in first source | ||
| diaveridine | diaveridine : An aminopyrimidine in which the pyrimidine ring carries amino substituents at C-2 and C-4 and a 3,4-dimethoxybenzyl group at C-5. A folic acid antagonist, it is used as a synergist with sulfonamides against the parasitic Eimeria species. diaveridine: RN given refers to parent cpd; structure | aminopyrimidine | antiparasitic agent; drug allergen |
| piritrexim | piritrexim: RN given refers to parent cpd; structure given in first source | ||
| brequinar | brequinar : A quinolinemonocarboxylic acid that is quinoline substituted by 2'-fluoro[1,1'-biphenyl]-4-yl, methyl, carboxy and fluoro groups at positions 2, 3, 4, and 6, respectively. It is an inhibitor of dihydroorotate dehydrogenase, an enzyme that is required for de novo pyrimidine biosynthesis. The compound exhibits antineoplastic and antiviral properties. | biphenyls; monocarboxylic acid; monofluorobenzenes; quinolinemonocarboxylic acid | anticoronaviral agent; antimetabolite; antineoplastic agent; antiviral agent; EC 1.3.5.2 [dihydroorotate dehydrogenase (quinone)] inhibitor; immunosuppressive agent; pyrimidine synthesis inhibitor |
| 2'-deoxyuridylic acid | 2'-deoxyuridylic acid: RN given refers to parent cpd | deoxyuridine phosphate; pyrimidine 2'-deoxyribonucleoside 5'-monophosphate | Escherichia coli metabolite; metabolite; mouse metabolite |
| 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 |
| 2,4-diaminopyrimidine | 2,6-diaminopyrimidine: structure in first source pyrimidine-2,4-diamine : An aminopyrimidine in which a pyrimidine nucleus is substituted with amino groups at C-2 and C-4. | aminopyrimidine | |
| epiroprim | epiroprim: an analog of trimethoprim with improved antimicrobial and pharmacokinetic properties; structure given in first source | ||
| sori 8895 | SoRI 8895: RN in first source | ||
| sori 8890 | SoRI 8890: RN in first source | ||
| dansyl hydrazine | |||
| 10-deazaaminopterin | |||
| epicatechin gallate | (-)-epicatechin-3-O-gallate : A gallate ester obtained by formal condensation of the carboxy group of gallic acid with the (3R)-hydroxy group of epicatechin. A natural product found in Parapiptadenia rigida. epicatechin gallate: a steroid 5alpha-reductase inhibitor; RN given refers to the (cis)-isomer; structure given in first source; isolated from green tea | catechin; gallate ester; polyphenol | EC 3.2.1.1 (alpha-amylase) inhibitor; EC 3.2.1.20 (alpha-glucosidase) inhibitor; metabolite |
| wr 99210 | BRL 6231: RN given refers to parent cpd; NM & N1 refer to HCl; synonym BRL 51084 refers to (mono-HBr); structure | ||
| methotrexate | dicarboxylic acid; monocarboxylic acid amide; pteridines | abortifacient; antimetabolite; antineoplastic agent; antirheumatic drug; dermatologic drug; DNA synthesis inhibitor; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; immunosuppressive agent | |
| 10-propargyl-10-deazaaminopterin | 10-propargyl-10-deazaaminopterin: structure in first source pralatrexate : A pteridine that is the N-4-[1-(2,4-diaminopteridin-6-yl)pent-4-yn-2-yl]benzoyl derivative of L-glutamic acid. Used for treatment of Peripheral T-Cell Lymphoma, an aggressive form of non-Hodgkins lymphoma. | N-acyl-L-glutamic acid; pteridines; terminal acetylenic compound | antimetabolite; antineoplastic agent; EC 1.5.1.3 (dihydrofolate reductase) inhibitor |
| naproxen | naproxen : A methoxynaphthalene that is 2-methoxynaphthalene substituted by a carboxy ethyl group at position 6. Naproxen is a non-steroidal anti-inflammatory drug commonly used for the reduction of pain, fever, inflammation and stiffness caused by conditions such as osteoarthritis, kidney stones, rheumatoid arthritis, psoriatic arthritis, gout, ankylosing spondylitis, menstrual cramps, tendinitis, bursitis, and for the treatment of primary dysmenorrhea. It works by inhibiting both the COX-1 and COX-2 enzymes. Naproxen: An anti-inflammatory agent with analgesic and antipyretic properties. Both the acid and its sodium salt are used in the treatment of rheumatoid arthritis and other rheumatic or musculoskeletal disorders, dysmenorrhea, and acute gout. | methoxynaphthalene; monocarboxylic acid | antipyretic; cyclooxygenase 1 inhibitor; cyclooxygenase 2 inhibitor; drug allergen; environmental contaminant; gout suppressant; non-narcotic analgesic; non-steroidal anti-inflammatory drug; xenobiotic |
| n-(4-(n-((2,4-diaminofuro(2,3-d)pyrimidin-5-yl)methyl)amino)benzoyl)glutamic acid | N-(4-(N-((2,4-diaminofuro(2,3-d)pyrimidin-5-yl)methyl)amino)benzoyl)glutamic acid: structure given in first source | ||
| n-4-hydroxy-2'-deoxycytidylic acid | N-4-hydroxy-2'-deoxycytidylic acid: reversibly binds to thymidylate synthetase | ||
| aminopterin | Aminopterin: A folic acid derivative used as a rodenticide that has been shown to be teratogenic. | dicarboxylic acid | EC 1.5.1.3 (dihydrofolate reductase) inhibitor; mutagen |
| 4-aminobenzoylglutamic acid | 4-aminobenzoylglutamic acid: RN given refers to (L)-isomer N-(4-aminobenzoyl)-L-glutamic acid : A dipeptide resulting from the formal condensation of the carboxylic acid group of 4-aminobenzoic acid with the amino group of L-glutamic acid. | dicarboxylic acid; dipeptide; N-acyl-L-alpha-amino acid; substituted aniline | |
| iclaprim | 5-[(2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl)methyl]pyrimidine-2,4-diamine : An aminopyrimidine that is 5-methylpyrimidine-2,4-diamine in which one of the hydrogens of the methyl group has been replaced by a 2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl group. iclaprim : A racemate consisting of equimolar amounts of (R)- and (S)-iclaprim. Both enantiomers exhibit similar, potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive and -resistant Staphylococcus aureus (MSSA and MRSA, respectively). iclaprim: has antiviral activity | aminopyrimidine; chromenes; cyclopropanes | |
| chalcone | trans-chalcone : The trans-isomer of chalcone. | chalcone | EC 3.2.1.1 (alpha-amylase) inhibitor |
| flavin mononucleotide | flavin mononucleotide; vitamin B2 | bacterial metabolite; coenzyme; cofactor; human metabolite; mouse metabolite | |
| 1-methyltryptophan | 1-methyltryptophan : A tryptophan derivative that is tryptophan carrying a single methyl substituent at position 1 on the indole. 1-methyltryptophan: an immunomodulator | indolyl carboxylic acid | |
| semaxinib | semaxanib : An oxindole that is 3-methyleneoxindole in which one of the hydrogens of the methylene group is replaced by a 3,5-dimethylpyrrol-2-yl group. | olefinic compound; oxindoles; pyrroles | angiogenesis modulating agent; antineoplastic agent; EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor; vascular endothelial growth factor receptor antagonist |
| edatrexate | edatrexate: structure given in first source | glutamic acid derivative | |
| gentamicin sulfate | |||
| teriflunomide | (trifluoromethyl)benzenes; aromatic amide; enamide; enol; nitrile; secondary carboxamide | drug metabolite; EC 1.3.98.1 [dihydroorotate oxidase (fumarate)] inhibitor; hepatotoxic agent; non-steroidal anti-inflammatory drug; tyrosine kinase inhibitor | |
| folic acid | folcysteine: used to promote fertility in chickens vitamin B9 : Any B-vitamin that exhibits biological activity against vitamin B9 deficiency. Vitamin B9 refers to the many forms of folic acid and its derivatives, including tetrahydrofolic acid (the active form), methyltetrahydrofolate (the primary form found in blood), methenyltetrahydrofolate, folinic acid amongst others. They are present in abundance in green leafy vegetables, citrus fruits, and animal products. Lack of vitamin B9 leads to anemia, a condition in which the body cannot produce sufficient number of red blood cells. Symptoms of vitamin B9 deficiency include fatigue, muscle weakness, and pale skin. | folic acids; N-acyl-amino acid | human metabolite; mouse metabolite; nutrient |
| raltitrexed | N-acyl-amino acid | ||
| nolatrexed | nolatrexed: structure given in first source; RN given refers to dihydrochloride | ||
| ici 198583 | ICI 198583: RN & structure given in first source | ||
| n-(4(n-((2-amino-4-hydroxy-6-quinazolinyl)methyl)prop-2-ynylamino)benzoyl)-l-glutamic acid | |||
| leucovorin | 5-formyltetrahydrofolic acid : A formyltetrahydrofolic acid in which the formyl group is located at position 5. | formyltetrahydrofolic acid | Escherichia coli metabolite; mouse metabolite |
| 1843u89 | 1843U89: structure given in first source; a folate analog | ||
| 5,11-methenyltetrahydrohomofolate | |||
| pemetrexed | pemetrexed disodium : An organic sodium salt that is the disodium salt of N-{4-[2-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}-L-glutamic acid. Inhibits thymidylate synthase (TS), 421 dihydrofolate reductase (DHFR), and glycinamide ribonucleotide formyltransferase (GARFT). | N-acyl-L-glutamic acid; pyrrolopyrimidine | antimetabolite; antineoplastic agent; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; EC 2.1.1.45 (thymidylate synthase) inhibitor; EC 2.1.2.2 (phosphoribosylglycinamide formyltransferase) inhibitor |
| n(10)-methylfolate | folic acids | ||
| cb 3717 | N-acyl-L-glutamic acid | ||
| (5)n,(8)n-deaza-(10)-n-methylfolate | |||
| cb 30865 | |||
| ag 85 | AG 85: structure given in first source | ||
| cb 3705 | CB 3705: inhibitor of dihydrofolate reductase & thymidylate synthetase | ||
| 2-desamino-2-methyl-5,8-dideazaisofolic acid | 2-desamino-2-methyl-5,8-dideazaisofolic acid: structure given in first source | ||
| (5)n,(8)n-deaza-(10)-n-methylfolate | (5)N,(8)N-deaza-(10)-N-methylfolate: structure |