2.0 2012-05-31 13:03:42 -0600 2015-10-15 16:13:48 -0600 ECMDB01031 M2MDB000230 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. 2-Deoxy-a-D-ribose 5-phosphate 2-Deoxy-a-D-ribose 5-phosphoric acid 2-Deoxy-a-delta-ribose 5-phosphate 2-Deoxy-a-delta-ribose 5-phosphoric acid 2-Deoxy-a-δ-ribose 5-phosphate 2-Deoxy-a-δ-ribose 5-phosphoric acid 2-Deoxy-alpha-D-ribose 5-phosphate 2-Deoxy-alpha-D-ribose 5-phosphoric acid 2-Deoxy-alpha-delta-ribose 5-phosphate 2-Deoxy-alpha-delta-ribose 5-phosphoric acid 2-Deoxy-D-ribose 5-phosphate 2-Deoxy-D-ribose 5-phosphoric acid 2-Deoxy-D-ribose-5-phosphate 2-Deoxy-D-ribose-5-phosphoric acid 2-Deoxy-α-D-ribose 5-phosphate 2-Deoxy-α-D-ribose 5-phosphoric acid 2-Deoxy-α-δ-ribose 5-phosphate 2-Deoxy-α-δ-ribose 5-phosphoric acid 2-Deoxyribose 5-phosphate 2-Deoxyribose 5-phosphoric acid 2-Deoxyribose-5-p 2-Deoxyribose-5-phosphate 2-Deoxyribose-5-phosphoric acid Deoxy-ribose-5p Deoxyribose 5-phosphate Deoxyribose 5-phosphoric acid Deoxyribose-5-p Deoxyribose-5-phosphate Deoxyribose-5-phosphoric acid DR5P C5H11O7P 214.1104 214.024239218 {[(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid [(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxyphosphonic acid 102916-66-5 O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1 InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1 KKZFLSZAWCYPOC-VPENINKCSA-N Solid Cytosol logp -2.14 ALOGPS logs -0.76 ALOGPS solubility 3.75e+01 g/l ALOGPS logp -1.5 ChemAxon pka_strongest_acidic 1.23 ChemAxon pka_strongest_basic -3.3 ChemAxon iupac {[(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid ChemAxon average_mass 214.1104 ChemAxon mono_mass 214.024239218 ChemAxon smiles O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1 ChemAxon formula C5H11O7P ChemAxon inchi InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1 ChemAxon inchikey KKZFLSZAWCYPOC-VPENINKCSA-N ChemAxon polar_surface_area 116.45 ChemAxon refractivity 39.32 ChemAxon polarizability 17.2 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 pyrimidine deoxyribonucleosides degradation PWY0-1298 purine deoxyribonucleosides degradation PWY0-1297 Specdb::MsMs 24929 Specdb::MsMs 24930 Specdb::MsMs 24931 Specdb::MsMs 31487 Specdb::MsMs 31488 Specdb::MsMs 31489 HMDB01031 635 25057464 C00673 16132 DEOXY-RIBOSE-5P 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). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Method of preparing 2-deoxyribose 5-phosphate US Patent http://hmdb.ca/system/metabolites/msds/000/000/926/original/HMDB01031.pdf?1358463351 Phosphopentomutase P0A6K6 DEOB_ECOLI deoB http://ecmdb.ca/proteins/P0A6K6.xml Deoxyribose-phosphate aldolase P0A6L0 DEOC_ECOLI deoC http://ecmdb.ca/proteins/P0A6L0.xml Ribokinase P0A9J6 RBSK_ECOLI rbsK http://ecmdb.ca/proteins/P0A9J6.xml Deoxyribose 5-phosphate <> Acetaldehyde + D-Glyceraldehyde 3-phosphate R01066 DEOXYRIBOSE-P-ALD-RXN Deoxyribose 1-phosphate <> Deoxyribose 5-phosphate R02749 D-PPENTOMUT-RXN Deoxyribose 5-phosphate + ADP <> Deoxyribose + Adenosine triphosphate R02750 2-deoxy-alpha-D-ribose 1-phosphate > Deoxyribose 5-phosphate Deoxyribose 5-phosphate > D-Glyceraldehyde 3-phosphate + Acetaldehyde Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose Shake flask and filter culture 303.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 1212000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621