Gene Association: DNPH1
UniProt Search:
DNPH1 (PROTEIN_CODING)
Function Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
found 12 associated metabolites with current gene based on the text mining result from the pubmed database.
5-Hydroxymethyluracil
5-Hydroxymethyluracil (5hmU), also known as alpha-hydroxythymine, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5hmU has been identified as a thymine base modification found in the genomes of a diverse range of organisms (PMID: 28137275). 5-hydroxymethyluracil has been detected in bacteriophages, dinoflagellates, leishmania, and in eukaryotic genomes where its level appears to be cell type-specific. 5-Hydroxymethyluracil arises from the oxidation of thymine. 5-Hydroxymethyluracil is produced by the enzyme thymine dioxygenase (EC 1.14.11.6) which catalyzes the chemical reaction thymine + 2-oxoglutarate + O2 <-> 5-hydroxymethyluracil + succinate + CO2. The 3 substrates of this enzyme are thymine, 2-oxoglutarate, and O2, whereas its 3 products are 5-hydroxymethyluracil, succinate, and CO2. The 5hmU base can also be generated by oxidation/hydroxylation of thymine by the Ten-Eleven-Translocation (TET) proteins or result from deamination of 5hmC (PMID: 29184924). DNA containing 5hmU has been reported to be more flexible and hydrophilic (PMID: 29184924). 5-Hydroxymethyluracil is an oxidation damage product derived from thymine or 5-methylcytosine. It is a product of thymine dioxygenase [EC 1.14.11.6]. (KEGG) D005765 - Gastrointestinal Agents > D000897 - Anti-Ulcer Agents D007155 - Immunologic Factors 5-Hydroxymethyluracil is a product of oxidative DNA damage. 5-Hydroxymethyluracil can be used as a potential epigenetic mark enhancing or inhibiting transcription with bacterial RNA polymerase. 5-Hydroxymethyluracil is a product of oxidative DNA damage. 5-Hydroxymethyluracil can be used as a potential epigenetic mark enhancing or inhibiting transcription with bacterial RNA polymerase.
2'-Deoxyguanosine 5'-monophosphate
2-Deoxyguanosine 5-monophosphate, also known as deoxyguanylic acid or 2-deoxy-GMP, belongs to the class of organic compounds known as purine 2-deoxyribonucleoside monophosphates. These are purine nucleotides with monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. 2-Deoxyguanosine 5-monophosphate is a purine 2-deoxyribonucleoside 5-monophosphate having guanine as the nucleobase. It exists in all living species, ranging from bacteria to humans. Within humans, 2-deoxyguanosine 5-monophosphate participates in a number of enzymatic reactions. In particular, 2-deoxyguanosine 5-monophosphate can be converted into dGDP which is mediated by the enzyme guanylate kinase. In addition, 2-deoxyguanosine 5-monophosphate can be converted into deoxyguanosine through its interaction with the enzyme cytosolic purine 5-nucleotidase. In humans, 2-deoxyguanosine 5-monophosphate is involved in the metabolic disorder called the gout or kelley-seegmiller syndrome pathway. 2-Deoxyguanosine 5-monophosphate is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2 carbon on the nucleotides pentose has been removed (hence the deoxy- part of the name). Additionally, the diphosphate of the name indicates that two of the phosphoryl groups of GTP have been removed, most likely by hydrolysis . [HMDB] Acquisition and generation of the data is financially supported in part by CREST/JST. COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS
2'-Deoxyuridine 5'-monophosphate disodium salt
Deoxyuridine monophosphate (dUMP), also known as deoxyuridylic acid or deoxyuridylate in its conjugate acid and conjugate base forms, respectively, is a deoxynucleotide. It belongs to the class of organic compounds known as pyrimidine 2-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dUMP exists in all living species, ranging from bacteria to humans. Within humans, dUMP participates in a number of enzymatic reactions. In particular, dUMP can be biosynthesized from dCMP through its interaction with the enzyme deoxycytidylate deaminase. In addition, dUMP can be biosynthesized from deoxyuridine; which is mediated by the enzyme thymidine kinase, cytosolic. In humans, dUMP is involved in pyrimidine metabolism. A pyrimidine 2-deoxyribonucleoside 5-monophosphate having uracil as the nucleobase. Outside of the human body, dUMP has been detected, but not quantified in several different foods, such as breadnut tree seeds, sea-buckthornberries, sour cherries, black walnuts, and common oregano. dUMP is formed by the reduction of ribonucleotides to deoxyribonucleotides by ribonucleoside diphosphate reductase [EC 1.17.4.1]. dUMP by the action of by thymidylate synthetase [EC 2.1.1.45] produces dTMP (5,10-Methylene-5,6,7,8-tetrahydrofolate is a cofactor for the reaction). The nuclear form of uracil-DNA glycosylase (UNG2), that its major role is to remove misincorporated dUMP residues (cells deficient in removal of misincorporated dUMP accumulate uracil residues). (PMID 11554311) [HMDB]. dUMP is found in many foods, some of which are ginger, evergreen huckleberry, vanilla, and common walnut. dUMP. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=964-26-1 (retrieved 2024-07-15) (CAS RN: 964-26-1). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0).
Deoxyribose 5-phosphate
Deoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source. [HMDB] Deoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source. Acquisition and generation of the data is financially supported in part by CREST/JST. KEIO_ID D026
isopentenyl adenosine
Riboprine, also known as isopentenyladenosine or ipa, is a member of the class of compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Riboprine is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). Riboprine can be found in a number of food items such as peppermint, chinese mustard, custard apple, and green bean, which makes riboprine a potential biomarker for the consumption of these food products. C274 - Antineoplastic Agent > C186664 - Cytotoxic Chemotherapeutic Agent > C272 - Antimetabolite D006133 - Growth Substances > D010937 - Plant Growth Regulators > D003583 - Cytokinins Acquisition and generation of the data is financially supported in part by CREST/JST. Same as: D05726 N6-Isopentenyladenosine (Riboprine), an RNA modification found in cytokinins, which regulate plant growth/differentiation, and a subset of tRNAs, where it improves the efficiency and accuracy of translation. N6-Isopentenyladenosine, an end product of the mevalonate pathway, is an autophagy inhibitor with an interesting anti-melanoma activity[1][2][3].
2-Deoxy-5-Guanylic Acid
COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS relative retention time with respect to 9-anthracene Carboxylic Acid is 0.057 relative retention time with respect to 9-anthracene Carboxylic Acid is 0.055
5-Hydroxymethyluracil
A primary alcohol that is uracil bearing a hydroxymethyl substituent at the 5-position. D005765 - Gastrointestinal Agents > D000897 - Anti-Ulcer Agents D007155 - Immunologic Factors 5-Hydroxymethyluracil is a product of oxidative DNA damage. 5-Hydroxymethyluracil can be used as a potential epigenetic mark enhancing or inhibiting transcription with bacterial RNA polymerase. 5-Hydroxymethyluracil is a product of oxidative DNA damage. 5-Hydroxymethyluracil can be used as a potential epigenetic mark enhancing or inhibiting transcription with bacterial RNA polymerase.
Riboprine
C274 - Antineoplastic Agent > C186664 - Cytotoxic Chemotherapeutic Agent > C272 - Antimetabolite D006133 - Growth Substances > D010937 - Plant Growth Regulators > D003583 - Cytokinins Same as: D05726 CONFIDENCE standard compound; INTERNAL_ID 306 N6-Isopentenyladenosine (Riboprine), an RNA modification found in cytokinins, which regulate plant growth/differentiation, and a subset of tRNAs, where it improves the efficiency and accuracy of translation. N6-Isopentenyladenosine, an end product of the mevalonate pathway, is an autophagy inhibitor with an interesting anti-melanoma activity[1][2][3].
