2.0 2012-05-31 13:02:34 -0600 2015-09-17 15:41:06 -0600 ECMDB00960 M2MDB000209 dGDP Deoxyguanosine diphosphate or dGDP is a member of the chemical class known as Purine 2'-deoxyribonucleoside Diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. DGDP is invovled in Purine metabolism. It is related to the common nucleic acid GTP, or guanosine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than GTP. 2'-Deoxy-GDP 2'-Deoxyguanosine-5'-diphosphate 2'-Deoxyguanosine-5'-diphosphoric acid 5'-dGDP Deoxyguanosine 5'-diphosphate Deoxyguanosine 5'-diphosphoric acid Deoxyguanosine diphosphate Deoxyguanosine diphosphoric acid Deoxyguanosine-diphosphate Deoxyguanosine-diphosphoric acid DGDP C10H15N5O10P2 427.2011 427.029414749 [({[5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid deoxyguanosine diphosphate 102783-74-4 NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1 InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 CIKGWCTVFSRMJU-KVQBGUIXSA-N Cytosol logp -1.44 ALOGPS logs -2.10 ALOGPS solubility 3.37e+00 g/l ALOGPS logp -2.8 ChemAxon pka_strongest_acidic 1.71 ChemAxon pka_strongest_basic 2.57 ChemAxon iupac [({[5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid ChemAxon average_mass 427.2011 ChemAxon mono_mass 427.029414749 ChemAxon smiles NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1 ChemAxon formula C10H15N5O10P2 ChemAxon inchi InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 ChemAxon inchikey CIKGWCTVFSRMJU-KVQBGUIXSA-N ChemAxon polar_surface_area 228.05 ChemAxon refractivity 84.42 ChemAxon polarizability 34.81 ChemAxon rotatable_bond_count 6 ChemAxon acceptor_count 12 ChemAxon donor_count 6 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon purine nucleotides de novo biosynthesis The biosynthesis of purine nucleotides is a complex process that begins with a phosphoribosyl pyrophosphate. This compound interacts with water and L-glutamine through a amidophosphoribosyl transferase resulting in a pyrophosphate, L-glutamic acid and a 5-phosphoribosylamine. The latter compound proceeds to interact with a glycine through an ATP driven phosphoribosylamine-glycine ligase resulting in the addition of glycine to the compound. This reaction releases an ADP, a phosphate, a hydrogen ion and a N1-(5-phospho-β-D-ribosyl)glycinamide. The latter compound interacts with formic acid, through an ATP driven phosphoribosylglycinamide formyltransferase 2 resulting in a phosphate, an ADP, a hydrogen ion and a 5-phosphoribosyl-N-formylglycinamide. The latter compound interacts with L-glutamine, and water through an ATP-driven phosphoribosylformylglycinamide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion, a L-glutamic acid and a 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine. The latter compound interacts with an ATP driven phosphoribosylformylglycinamide cyclo-ligase resulting in a release of ADP, a phosphate, a hydrogen ion and a 5-aminoimidazole ribonucleotide. The latter compound interacts with a hydrogen carbonate through an ATP driven N5-carboxyaminoimidazole ribonucleotide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion and a N5-carboxyaminoimidazole ribonucleotide.The latter compound then interacts with a N5-carboxyaminoimidazole ribonucleotide mutase resulting in a 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This compound interacts with an L-aspartic acid through an ATP driven phosphoribosylaminoimidazole-succinocarboxamide synthase resulting in a phosphate, an ADP, a hydrogen ion and a SAICAR. SAICAR interacts with an adenylosuccinate lyase resulting in a fumaric acid and an AICAR. AICAR interacts with a formyltetrahydrofolate through a AICAR transformylase / IMP cyclohydrolase resulting in a release of a tetrahydropterol mono-l-glutamate and a FAICAR. The latter compound, FAICAR, interacts in a reversible reaction through a AICAR transformylase / IMP cyclohydrolase resulting in a release of water and Inosinic acid. Inosinic acid can be metabolized to produce dGTP and dATP three different methods each. dGTP: Inosinic acid, water and NAD are processed by IMP dehydrogenase resulting in a release of NADH, a hydrogen ion and Xanthylic acid. Xanthylic acid interacts with L-glutamine, and water through an ATP driven GMP synthetase resulting in pyrophosphate, AMP, L-glutamic acid, a hydrogen ion and Guanosine monophosphate. The latter compound is the phosphorylated by reacting with an ATP driven guanylate kinase resulting in a release of ADP and a Gaunosine diphosphate. Guanosine diphosphate can be metabolized in three different ways: 1.-Guanosine diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and a Guanosine triphosphate. This compound interacts with a reduced flavodoxin protein through a ribonucleoside-triphosphate reductase resulting in a oxidized flavodoxin a water moleculer and a dGTP 2.-Guanosine diphosphate interacts with a reduced NrdH glutaredoxin-like proteins through a ribonucleoside-diphosphate reductase 2 resulting in the release of an oxidized NrdH glutaredoxin-like protein, a water molecule and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. 3.-Guanosine diphosphate interacts with a reduced thioredoxin ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. dATP: Inosinic acid interacts with L-aspartic acid through an GTP driven adenylosuccinate synthase results in the release of GDP, a hydrogen ion, a phosphate and N(6)-(1,2-dicarboxyethyl)AMP. The latter compound is then cleaved by a adenylosuccinate lyase resulting in a fumaric acid and an Adenosine monophosphate. This compound is then phosphorylated by an adenylate kinase resulting in the release of ATP and an adenosine diphosphate. Adenosine diphosphate can be metabolized in three different ways: 1.-Adenosine diphosphate is involved in a reversible reaction by interacting with a hydrogen ion and a phosphate through a ATP synthase / thiamin triphosphate synthase resulting in a hydrogen ion, a water molecule and an Adenosine triphosphate. The adenosine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in an oxidized flavodoxin, a water molecule and a dATP 2.- Adenosine diphosphate interacts with an reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, a oxidized thioredoxin and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP 3.- Adenosine diphosphate interacts with an reduced NrdH glutaredoxin-like protein through a ribonucleoside diphosphate reductase 2 resulting in a release of a water molecule, a oxidized glutaredoxin-like protein and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP PW000910 Metabolic purine nucleotides de novo biosynthesis 1435709748 PW000960 Metabolic purine nucleotides de novo biosynthesis 2 The biosynthesis of purine nucleotides is a complex process that begins with a phosphoribosyl pyrophosphate. This compound interacts with water and L-glutamine through a amidophosphoribosyl transferase resulting in a pyrophosphate, L-glutamic acid and a 5-phosphoribosylamine. The latter compound proceeds to interact with a glycine through an ATP driven phosphoribosylamine-glycine ligase resulting in the addition of glycine to the compound. This reaction releases an ADP, a phosphate, a hydrogen ion and a N1-(5-phospho-β-D-ribosyl)glycinamide. The latter compound interacts with formic acid, through an ATP driven phosphoribosylglycinamide formyltransferase 2 resulting in a phosphate, an ADP, a hydrogen ion and a 5-phosphoribosyl-N-formylglycinamide. The latter compound interacts with L-glutamine, and water through an ATP-driven phosphoribosylformylglycinamide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion, a L-glutamic acid and a 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine. The latter compound interacts with an ATP driven phosphoribosylformylglycinamide cyclo-ligase resulting in a release of ADP, a phosphate, a hydrogen ion and a 5-aminoimidazole ribonucleotide. The latter compound interacts with a hydrogen carbonate through an ATP driven N5-carboxyaminoimidazole ribonucleotide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion and a N5-carboxyaminoimidazole ribonucleotide(5-Phosphoribosyl-5-carboxyaminoimidazole).The latter compound then interacts with a N5-carboxyaminoimidazole ribonucleotide mutase resulting in a 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This compound interacts with an L-aspartic acid through an ATP driven phosphoribosylaminoimidazole-succinocarboxamide synthase resulting in a phosphate, an ADP, a hydrogen ion and a SAICAR. SAICAR interacts with an adenylosuccinate lyase resulting in a fumaric acid and an AICAR. AICAR interacts with a formyltetrahydrofolate through a AICAR transformylase / IMP cyclohydrolase resulting in a release of a tetrahydropterol mono-l-glutamate and a FAICAR. The latter compound, FAICAR, interacts in a reversible reaction through a AICAR transformylase / IMP cyclohydrolase resulting in a release of water and Inosinic acid. Inosinic acid can be metabolized to produce dGTP and dATP three different methods each. dGTP: Inosinic acid, water and NAD are processed by IMP dehydrogenase resulting in a release of NADH, a hydrogen ion and Xanthylic acid. Xanthylic acid interacts with L-glutamine, and water through an ATP driven GMP synthetase resulting in pyrophosphate, AMP, L-glutamic acid, a hydrogen ion and Guanosine monophosphate. The latter compound is the phosphorylated by reacting with an ATP driven guanylate kinase resulting in a release of ADP and a Gaunosine diphosphate. Guanosine diphosphate can be metabolized in three different ways: 1.-Guanosine diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and a Guanosine triphosphate. This compound interacts with a reduced flavodoxin protein through a ribonucleoside-triphosphate reductase resulting in a oxidized flavodoxin a water moleculer and a dGTP 2.-Guanosine diphosphate interacts with a reduced NrdH glutaredoxin-like proteins through a ribonucleoside-diphosphate reductase 2 resulting in the release of an oxidized NrdH glutaredoxin-like protein, a water molecule and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. 3.-Guanosine diphosphate interacts with a reduced thioredoxin ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. dATP: Inosinic acid interacts with L-aspartic acid through an GTP driven adenylosuccinate synthase results in the release of GDP, a hydrogen ion, a phosphate and N(6)-(1,2-dicarboxyethyl)AMP. The latter compound is then cleaved by a adenylosuccinate lyase resulting in a fumaric acid and an Adenosine monophosphate. This compound is then phosphorylated by an adenylate kinase resulting in the release of ATP and an adenosine diphosphate. Adenosine diphosphate can be metabolized in three different ways: 1.-Adenosine diphosphate is involved in a reversible reaction by interacting with a hydrogen ion and a phosphate through a ATP synthase / thiamin triphosphate synthase resulting in a hydrogen ion, a water molecule and an Adenosine triphosphate. The adenosine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in an oxidized flavodoxin, a water molecule and a dATP 2.- Adenosine diphosphate interacts with an reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, a oxidized thioredoxin and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP 3.- Adenosine diphosphate interacts with an reduced NrdH glutaredoxin-like protein through a ribonucleoside diphosphate reductase 2 resulting in a release of a water molecule, a oxidized glutaredoxin-like protein and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP PW002033 Metabolic guanosine nucleotides <i>de novo</i> biosynthesis PWY-6125 Specdb::MsMs 23528 Specdb::MsMs 23529 Specdb::MsMs 23530 Specdb::MsMs 30326 Specdb::MsMs 30327 Specdb::MsMs 30328 HMDB00960 624 C00361 DGDP 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 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 Ribonucleoside-diphosphate reductase 1 subunit alpha P00452 RIR1_ECOLI nrdA http://ecmdb.ca/proteins/P00452.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Uridine kinase P0A8F4 URK_ECOLI udk http://ecmdb.ca/proteins/P0A8F4.xml Pyruvate kinase I P0AD61 KPYK1_ECOLI pykF http://ecmdb.ca/proteins/P0AD61.xml Thioredoxin-2 P0AGG4 THIO2_ECOLI trxC http://ecmdb.ca/proteins/P0AGG4.xml Pyruvate kinase II P21599 KPYK2_ECOLI pykA http://ecmdb.ca/proteins/P21599.xml Anaerobic ribonucleoside-triphosphate reductase P28903 NRDD_ECOLI nrdD http://ecmdb.ca/proteins/P28903.xml Ribonucleoside-diphosphate reductase 2 subunit beta P37146 RIR4_ECOLI nrdF http://ecmdb.ca/proteins/P37146.xml Ribonucleoside-diphosphate reductase 2 subunit alpha P39452 RIR3_ECOLI nrdE http://ecmdb.ca/proteins/P39452.xml Guanylate kinase P60546 KGUA_ECOLI gmk http://ecmdb.ca/proteins/P60546.xml Adenylate kinase P69441 KAD_ECOLI adk http://ecmdb.ca/proteins/P69441.xml Ribonucleoside-diphosphate reductase 1 subunit beta P69924 RIR2_ECOLI nrdB http://ecmdb.ca/proteins/P69924.xml Glutaredoxin-4 P0AC69 GLRX4_ECOLI grxD http://ecmdb.ca/proteins/P0AC69.xml Glutaredoxin-3 P0AC62 GLRX3_ECOLI grxC http://ecmdb.ca/proteins/P0AC62.xml Glutaredoxin-2 P0AC59 GLRX2_ECOLI grxB http://ecmdb.ca/proteins/P0AC59.xml Glutaredoxin-1 P68688 GLRX1_ECOLI grxA http://ecmdb.ca/proteins/P68688.xml Thioredoxin-1 P0AA25 THIO_ECOLI trxA http://ecmdb.ca/proteins/P0AA25.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Guanosine diphosphate + Reduced Thioredoxin > dGDP + Water + Oxidized Thioredoxin Guanosine diphosphate + glutaredoxin > dGDP + glutaredoxin + Water Adenosine triphosphate + dGDP <> ADP + dGTP R01857 DGDPKIN-RXN Adenosine triphosphate + 2'-Deoxyguanosine 5'-monophosphate <> ADP + dGDP R02090 GMKALT-RXN dGDP + Adenosine triphosphate > dGTP + ADP DGDPKIN-RXN dGDP + Adenosine triphosphate + dGDP > Adenosine diphosphate + dGTP + ADP PW_R003432 Guanosine diphosphate + reduced thioredoxin > oxidized thioredoxin + Water + dGDP + dGDP PW_R003431 Guanosine diphosphate + a reduced NrdH glutaredoxin-like protein > Water + an oxidized NrdH glutaredoxin-like protein + dGDP + dGDP PW_R003433 Adenosine triphosphate + dGDP <> ADP + dGTP Adenosine triphosphate + 2 2'-Deoxyguanosine 5'-monophosphate <> ADP + dGDP