2.0 2012-05-31 13:50:34 -0600 2015-06-03 15:53:57 -0600 ECMDB01351 M2MDB000350 Deoxyribose 1-phosphate Deoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase. 2-Deoxy-a-D-ribose 1-phosphate 2-Deoxy-a-D-ribose 1-phosphoric acid 2-Deoxy-a-delta-ribose 1-phosphate 2-Deoxy-a-delta-ribose 1-phosphoric acid 2-Deoxy-a-δ-ribose 1-phosphate 2-Deoxy-a-δ-ribose 1-phosphoric acid 2-Deoxy-alpha-D-ribose 1-phosphate 2-Deoxy-alpha-D-ribose 1-phosphoric acid 2-Deoxy-alpha-delta-ribose 1-phosphate 2-Deoxy-alpha-delta-ribose 1-phosphoric acid 2-Deoxy-D-erythro-pentofuranose 1-phosphate 2-Deoxy-D-erythro-pentofuranose 1-phosphoric acid 2-Deoxy-D-ribose 1-phosphate 2-Deoxy-D-ribose 1-phosphoric acid 2-Deoxy-D-ribose-1-phosphate 2-Deoxy-D-ribose-1-phosphoric acid 2-Deoxy-delta-erythro-pentofuranose 1-phosphate 2-Deoxy-delta-erythro-pentofuranose 1-phosphoric acid 2-Deoxy-delta-ribose 1-phosphate 2-Deoxy-delta-ribose 1-phosphoric acid 2-Deoxy-delta-ribose-1-phosphate 2-Deoxy-delta-ribose-1-phosphoric acid 2-Deoxy-α-D-ribose 1-phosphate 2-Deoxy-α-D-ribose 1-phosphoric acid 2-Deoxy-α-δ-ribose 1-phosphate 2-Deoxy-α-δ-ribose 1-phosphoric acid 2-Deoxy-δ-erythro-pentofuranose 1-phosphate 2-Deoxy-δ-erythro-pentofuranose 1-phosphoric acid 2-Deoxy-δ-ribose 1-phosphate 2-Deoxy-δ-ribose 1-phosphoric acid 2-Deoxy-δ-ribose-1-phosphate 2-Deoxy-δ-ribose-1-phosphoric acid 2-Deoxyribofuranose 1-phosphate 2-Deoxyribofuranose 1-phosphoric acid D-2-Deoxy-ribofuranose 1-phosphate D-2-Deoxy-ribofuranose 1-phosphoric acid Delta-2-Deoxy-ribofuranose 1-phosphate delta-2-Deoxy-ribofuranose 1-phosphoric acid Deoxy-D-ribose 1-phosphate Deoxy-D-ribose 1-phosphoric acid Deoxyribose 1-phosphate Deoxyribose 1-phosphoric acid Deoxyribose-1-phosphate Deoxyribose-1-phosphoric acid DR1P δ-2-Deoxy-ribofuranose 1-phosphate δ-2-Deoxy-ribofuranose 1-phosphoric acid C5H11O7P 214.1104 214.024239218 {[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid deoxyribose-1-phosphate 17210-42-3 OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1 KBDKAJNTYKVSEK-PYHARJCCSA-N Solid Cytosol logp -2.14 ALOGPS logs -0.76 ALOGPS solubility 3.76e+01 g/l ALOGPS logp -1.5 ChemAxon pka_strongest_acidic 1.37 ChemAxon pka_strongest_basic -3 ChemAxon iupac {[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid ChemAxon average_mass 214.1104 ChemAxon mono_mass 214.024239218 ChemAxon smiles OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O ChemAxon formula C5H11O7P ChemAxon inchi InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1 ChemAxon inchikey KBDKAJNTYKVSEK-PYHARJCCSA-N ChemAxon polar_surface_area 116.45 ChemAxon refractivity 39.32 ChemAxon polarizability 17.21 ChemAxon rotatable_bond_count 3 ChemAxon acceptor_count 6 ChemAxon donor_count 4 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Pentose phosphate pathway ec00030 Purine metabolism ec00230 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 Nicotinate and nicotinamide metabolism ec00760 Metabolic pathways eco01100 purine deoxyribonucleosides degradation PW002077 Metabolic 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 pyrimidine deoxyribonucleosides degradation PWY0-1298 purine deoxyribonucleosides degradation PWY0-1297 Specdb::CMs 3341 Specdb::CMs 38035 Specdb::CMs 153463 Specdb::NmrOneD 255108 Specdb::NmrOneD 255109 Specdb::NmrOneD 255110 Specdb::NmrOneD 255111 Specdb::NmrOneD 255112 Specdb::NmrOneD 255113 Specdb::NmrOneD 255114 Specdb::NmrOneD 255115 Specdb::NmrOneD 255116 Specdb::NmrOneD 255117 Specdb::NmrOneD 255118 Specdb::NmrOneD 255119 Specdb::NmrOneD 255120 Specdb::NmrOneD 255121 Specdb::NmrOneD 255122 Specdb::NmrOneD 255123 Specdb::NmrOneD 255124 Specdb::NmrOneD 255125 Specdb::NmrOneD 255126 Specdb::NmrOneD 255127 Specdb::MsMs 27293 Specdb::MsMs 27294 Specdb::MsMs 27295 Specdb::MsMs 33851 Specdb::MsMs 33852 Specdb::MsMs 33853 Specdb::MsMs 2301420 Specdb::MsMs 2301421 Specdb::MsMs 2301422 Specdb::MsMs 3063616 Specdb::MsMs 3063617 Specdb::MsMs 3063618 HMDB01351 439287 388420 C00672 28542 DEOXY-D-RIBOSE-1-PHOSPHATE Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. 17765195 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). 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Free Radic Biol Med. 1999 Jan;26(1-2):129-35. 9890648 Thymidine phosphorylase P07650 TYPH_ECOLI deoA http://ecmdb.ca/proteins/P07650.xml Phosphopentomutase P0A6K6 DEOB_ECOLI deoB http://ecmdb.ca/proteins/P0A6K6.xml Purine nucleoside phosphorylase deoD-type P0ABP8 DEOD_ECOLI deoD http://ecmdb.ca/proteins/P0ABP8.xml Uridine phosphorylase P12758 UDP_ECOLI udp http://ecmdb.ca/proteins/P12758.xml Xanthosine phosphorylase P45563 XAPA_ECOLI xapA http://ecmdb.ca/proteins/P45563.xml Deoxyinosine + Phosphate <> Deoxyribose 1-phosphate + Hypoxanthine R02748 Deoxyguanosine + Phosphate <> Deoxyribose 1-phosphate + Guanine R01969 Deoxyuridine + Phosphate <> Deoxyribose 1-phosphate + Uracil R02484 Phosphate + Thymidine <> Deoxyribose 1-phosphate + Thymine R01570 Deoxyribose 1-phosphate <> Deoxyribose 5-phosphate R02749 D-PPENTOMUT-RXN Deoxyadenosine + Phosphate <> Deoxyribose 1-phosphate + Adenine R02557 5-FU + Deoxyribose 1-phosphate <> 5-Fluorodeoxyuridine + Phosphate R08230 Purine nucleoside + Phosphate + Purine deoxyribonucleoside <> Purine + Ribose-1-phosphate + Deoxyribose 1-phosphate R08368 Deoxyribose 1-phosphate > Deoxyribose 5-phosphate PW_R006071 Deoxyuridine + Phosphate > Uracil + Deoxyribose 1-phosphate PW_R006018 Deoxyribose 1-phosphate + Thymine > Phosphate + Thymidine PW_R006019 Deoxyadenosine + Phosphate > Adenine + Deoxyribose 1-phosphate PW_R006069