2.0 2012-05-31 09:55:14 -0600 2015-09-13 12:56:05 -0600 ECMDB00012 M2MDB000002 Deoxyuridine 2'-Deoxyuridine is a naturally occurring nucleoside. It is similar in chemical structure to uridine, but without the 2'-hydroxyl group. It is considered to be an antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. 1-(2-Deoxy-b-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-b-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-b-delta-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-b-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-b-δ-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-b-δ-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione 1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione 1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione 1-(2-Deoxy-D-erythro-pentofuranosyl)uracil 1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil 1-(2-Deoxy-β-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-β-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-β-δ-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-β-δ-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 1-(2-Deoxy-δ-erythro-pentofuranosyl)uracil 2'-Deoxyuridine 2'-Desoxyuridine Deoxyribose uracil Desoxyuridine DUri Uracil deoxyriboside Uracil desoxyuridine C9H12N2O5 228.202 228.074621504 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione 2'-deoxyuridine 951-78-0 OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1 MXHRCPNRJAMMIM-SHYZEUOFSA-N Solid Cytosol Extra-organism Periplasm logp -1.49 ALOGPS logs -0.40 ALOGPS solubility 9.06e+01 g/l ALOGPS melting_point 167 oC logp -1.5 ChemAxon pka_strongest_acidic 9.71 ChemAxon pka_strongest_basic -3 ChemAxon iupac 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione ChemAxon average_mass 228.202 ChemAxon mono_mass 228.074621504 ChemAxon smiles OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O ChemAxon formula C9H12N2O5 ChemAxon inchi InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1 ChemAxon inchikey MXHRCPNRJAMMIM-SHYZEUOFSA-N ChemAxon polar_surface_area 99.1 ChemAxon refractivity 51.05 ChemAxon polarizability 21.06 ChemAxon rotatable_bond_count 2 ChemAxon acceptor_count 5 ChemAxon donor_count 3 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Pyrimidine metabolism The metabolism of pyrimidines begins with L-glutamine interacting with water molecule and a hydrogen carbonate through an ATP driven carbamoyl phosphate synthetase resulting in a hydrogen ion, an ADP, a phosphate, an L-glutamic acid and a carbamoyl phosphate. The latter compound interacts with an L-aspartic acid through a aspartate transcarbamylase resulting in a phosphate, a hydrogen ion and a N-carbamoyl-L-aspartate. The latter compound interacts with a hydrogen ion through a dihydroorotase resulting in the release of a water molecule and a 4,5-dihydroorotic acid. This compound interacts with an ubiquinone-1 through a dihydroorotate dehydrogenase, type 2 resulting in a release of an ubiquinol-1 and an orotic acid. The orotic acid then interacts with a phosphoribosyl pyrophosphate through a orotate phosphoribosyltransferase resulting in a pyrophosphate and an orotidylic acid. The latter compound then interacts with a hydrogen ion through an orotidine-5 '-phosphate decarboxylase, resulting in an release of carbon dioxide and an Uridine 5' monophosphate. The Uridine 5' monophosphate process to get phosphorylated by an ATP driven UMP kinase resulting in the release of an ADP and an Uridine 5--diphosphate. Uridine 5-diphosphate can be metabolized in multiple ways in order to produce a Deoxyuridine triphosphate. 1.-Uridine 5-diphosphate interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in the release of a water molecule and an oxidized thioredoxin and an dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 2.-Uridine 5-diphosphate interacts with a reduced NrdH glutaredoxin-like protein through a Ribonucleoside-diphosphate reductase 1 resulting in a release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 3.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate. The latter compound interacts with a reduced flavodoxin through ribonucleoside-triphosphate reductase resulting in the release of an oxidized flavodoxin, a water molecule and a Deoxyuridine triphosphate 4.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in the release of a water molecule, an oxidized flavodoxin and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 5.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP then interacts with a reduced NrdH glutaredoxin-like protein through a ribonucleoside-diphosphate reductase 2 resulting in the release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 6.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. The deoxyuridine triphosphate then interacts with a water molecule through a nucleoside triphosphate pyrophosphohydrolase resulting in a release of a hydrogen ion, a phosphate and a dUMP. The dUMP then interacts with a methenyltetrahydrofolate through a thymidylate synthase resulting in a dihydrofolic acid and a 5-thymidylic acid. Then 5-thymidylic acid is then phosphorylated through a nucleoside diphosphate kinase resulting in the release of an ADP and thymidine 5'-triphosphate. PW000942 ec00240 Metabolic Drug metabolism - other enzymes ec00983 Metabolic pathways eco01100 pyrimidine deoxyribonucleosides degradation The degradation of deoxycytidine starts with deoxycytidine being introduced into the cytosol through either a nupG or nupC symporter. Once inside, it can can be degrade through water,a hydrogen ion and a deoxycytidien deaminsa resultin in the release of a ammonium and a a deoxyuridine. The deoxyuridine is then degraded through a uracil phosphorylase resulting in the release of a deoxyribose 1-phosphate and a uracil. The degradation of thymidine starts with thymidine being introduced into the cytosol through either a nupG or nupC symporter. Thymidine is then degrades through a phosphorylase resulting in the release of a thymine and a deoxyribose 1-phosphate. PW002063 Metabolic salvage pathways of pyrimidine deoxyribonucleotides The pathway begins with the introduction of deoxycytidine into the cytosol, either through a nupG symporter or a nupC symporter. Once inside it is deaminated when reacting with a water molecule, a hydrogen ion and a deoxycytidine deaminase resulting in the release of an ammonium and a deoxyuridine. Deoxyuridine can also be imported through a nupG symporter or a nupC symporter. Deoxyuridine can react with an ATP through a deoxyuridine kinase resulting in the release of a ADP , a hydrogen ion and a dUMP. Deoxyuridine can also react with a phosphate through a uracil phosphorylase resulting in the release of a uracil and a deoxy-alpha-D-ribose 1-phosphate. This compound in turn reacts with a thymine through a thymidine phosphorylase resulting in the release of a phosphate and a thymidine. Thymidine in turn reacts with an ATP through a thymidine kinase resulting in a release of an ADP, a hydrogen ion and a dTMP PW002061 Metabolic salvage pathways of pyrimidine deoxyribonucleotides PWY0-181 pyrimidine deoxyribonucleosides degradation PWY0-1298 Specdb::CMs 280 Specdb::CMs 281 Specdb::CMs 1975 Specdb::CMs 1990 Specdb::CMs 7117 Specdb::CMs 30425 Specdb::CMs 30426 Specdb::CMs 30949 Specdb::CMs 30950 Specdb::CMs 37242 Specdb::CMs 150921 Specdb::CMs 1046889 Specdb::CMs 1046891 Specdb::CMs 1046893 Specdb::CMs 1046895 Specdb::CMs 1046897 Specdb::CMs 1046899 Specdb::CMs 1046901 Specdb::CMs 1046903 Specdb::CMs 1046905 Specdb::CMs 1046907 Specdb::CMs 1046909 Specdb::NmrOneD 1028 Specdb::NmrOneD 141870 Specdb::NmrOneD 141871 Specdb::NmrOneD 141872 Specdb::NmrOneD 141873 Specdb::NmrOneD 141874 Specdb::NmrOneD 141875 Specdb::NmrOneD 141876 Specdb::NmrOneD 141877 Specdb::NmrOneD 141878 Specdb::NmrOneD 141879 Specdb::NmrOneD 141880 Specdb::NmrOneD 141881 Specdb::NmrOneD 141882 Specdb::NmrOneD 141883 Specdb::NmrOneD 141884 Specdb::NmrOneD 141885 Specdb::NmrOneD 141886 Specdb::NmrOneD 141887 Specdb::NmrOneD 141888 Specdb::NmrOneD 141889 Specdb::MsMs 19 Specdb::MsMs 20 Specdb::MsMs 21 Specdb::MsMs 251793 Specdb::MsMs 251794 Specdb::MsMs 251795 Specdb::MsMs 271734 Specdb::MsMs 271735 Specdb::MsMs 271736 Specdb::MsMs 439582 Specdb::MsMs 439583 Specdb::MsMs 439584 Specdb::MsMs 439585 Specdb::MsMs 439586 Specdb::MsMs 439587 Specdb::MsMs 440069 Specdb::MsMs 449646 Specdb::MsMs 449647 Specdb::MsMs 2242699 Specdb::MsMs 2243154 Specdb::MsMs 2244845 Specdb::MsMs 2245283 Specdb::MsMs 2246883 Specdb::MsMs 2247397 Specdb::MsMs 2249020 Specdb::NmrTwoD 921 HMDB00012 13712 13118 C00526 16450 DEOXYURIDINE DUR Deoxyuridine Keseler, I. 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Synthetic Communications (1990), 20(7), 1039-46. http://hmdb.ca/system/metabolites/msds/000/000/007/original/HMDB00012.pdf?1358462809 Protein ushA P07024 USHA_ECOLI ushA http://ecmdb.ca/proteins/P07024.xml Thymidine phosphorylase P07650 TYPH_ECOLI deoA http://ecmdb.ca/proteins/P07650.xml Multifunctional protein surE P0A840 SURE_ECOLI surE http://ecmdb.ca/proteins/P0A840.xml 5'-nucleotidase yjjG P0A8Y1 YJJG_ECOLI yjjG http://ecmdb.ca/proteins/P0A8Y1.xml Cytidine deaminase P0ABF6 CDD_ECOLI cdd http://ecmdb.ca/proteins/P0ABF6.xml Purine nucleoside phosphorylase deoD-type P0ABP8 DEOD_ECOLI deoD http://ecmdb.ca/proteins/P0ABP8.xml Class B acid phosphatase P0AE22 APHA_ECOLI aphA http://ecmdb.ca/proteins/P0AE22.xml Uridine phosphorylase P12758 UDP_ECOLI udp http://ecmdb.ca/proteins/P12758.xml Thymidine kinase P23331 KITH_ECOLI tdk http://ecmdb.ca/proteins/P23331.xml 5'-nucleotidase yfbR P76491 YFBR_ECOLI yfbR http://ecmdb.ca/proteins/P76491.xml Nucleoside permease nupC P0AFF2 NUPC_ECOLI nupC http://ecmdb.ca/proteins/P0AFF2.xml Nucleoside permease nupG P0AFF4 NUPG_ECOLI nupG http://ecmdb.ca/proteins/P0AFF4.xml Nucleoside permease nupX P33021 NUPX_ECOLI nupX http://ecmdb.ca/proteins/P33021.xml Nucleoside-specific channel-forming protein tsx P0A927 TSX_ECOLI tsx http://ecmdb.ca/proteins/P0A927.xml dUMP + Water > Deoxyuridine + Phosphate Deoxyuridine + Phosphate <> Deoxyribose 1-phosphate + Uracil R02484 Adenosine triphosphate + Deoxyuridine > ADP + dUMP + Hydrogen ion R02099 DURIDKI-RXN Deoxycytidine + Hydrogen ion + Water > Deoxyuridine + Ammonium Adenosine triphosphate + Deoxyuridine <> ADP + dUMP R02099 Deoxycytidine + Water <> Deoxyuridine + Ammonia R02485 Deoxyuridine + Phosphate <> deoxyribose-1-phosphate + Uracil URA-PHOSPH-RXN Water + Deoxycytidine > Ammonia + Deoxyuridine R02485 CYTIDEAM-RXN Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine R01878 Deoxyuridine + Phosphate > Uracil + Deoxyribose 1-phosphate PW_R006018