{"ymdb_id":"YMDB00661","created_at":"2011-05-29T18:41:20.000Z","updated_at":"2016-09-08T18:35:45.000Z","name":"2-deoxy-D-ribose","cas":"533-67-5","state":"Solid","melting_point":"91 oC","description":"Deoxyribose, more, precisely 2-deoxyribose, is a monosaccharide. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom. Since the pentose sugars arabinose and ribose only differ by the stereochemistry at C2', 2-deoxyribose and 2-deoxyarabinose are equivalent, although the latter term is rarely used because ribose, not arabinose, is the precursor to deoxyribose. [Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"28816","hmdb_id":"HMDB03224","kegg_id":"C00672","pubchem_id":"10786","cs_id":"24765641","foodb_id":null,"wikipedia_link":"Deoxyribose","biocyc_id":"CPD-7298","iupac":"(3S,4R)-3,4,5-trihydroxypentanal","traditional_iupac":"deoxyribose","logp":"-2.222867160333333","pka":"13.421911653562585","alogps_solubility":"7.09e+02 g/l","alogps_logp":"-1.90","alogps_logs":"0.72","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"4","polar_surface_area":"77.76","refractivity":"30.044899999999995","polarizability":"12.7114814509769","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.9723451301813055","pka_strongest_acidic":"11.596483314248868","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2-Deoxy-alpha-D-ribose 1-phosphate","2-Deoxy-D-arabinose","2-Deoxy-D-erythro-pentose","2-Deoxy-D-ribohexopyranose","2-Deoxy-D-ribose","2-Deoxy-D-ribose 1-phosphate","2-Deoxypentose","2-Deoxyribose","2-Desoxy ribosoe","2'-Deoxy-D-ribose","D-2-Deoxyribose","D-2-Desoxyribose","D-dRib","D-Erythro-Pentose, 2-deoxy-","D-Ribose, 2-deoxy-","deoxy-ribose 1-phosphate","Deoxyribose","Ribose, 2-deoxy-, D-","Thyminose"],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"},{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"growth_conditions":[],"references":[{"pubmed_id":18846089,"citation":"Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). \"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.\" Nat Biotechnol 26:1155-1160."},{"pubmed_id":5640385,"citation":"Cirillo, V. P. (1968). \"Relationship between sugar structure and competition for the sugar transport system in Bakers' yeast.\" J Bacteriol 95:603-611."}],"proteins":[{"created_at":"2011-05-26T19:34:05.000Z","updated_at":"2011-07-22T17:54:35.000Z","name":"Probable ribokinase","uniprot_id":"P25332","uniprot_name":"RBSK_YEAST","enzyme":true,"transporter":false,"gene_name":"RBK1","num_residues":333,"molecular_weight":"36923.80078","theoretical_pi":"4.93","general_function":"Involved in phosphotransferase activity, alcohol group as acceptor","specific_function":"ATP + D-ribose = ADP + D-ribose 5-phosphate","reactions":[{"id":1445,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1944,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2579,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"ATP + D-ribose = ADP + D-ribose 5-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"X56909","genbank_protein_id":"4492","gene_card_id":"RBK1","chromosome_location":"chromosome 3","locus":"YCR036W","synonyms":[],"enzyme_classes":["2.7.1.15"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, alcohol group as acceptor"},{"category":"Function","description":" ribokinase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" alcohol metabolic process"},{"category":"Process","description":" monosaccharide metabolic process"},{"category":"Process","description":" pentose metabolic process"},{"category":"Process","description":" D-ribose metabolic process"}],"pfams":[{"name":"PfkB","identifier":"PF00294"}],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"}],"gene_sequence":"ATGGGTATTACAGTAATAGGTTCTCTAAACTATGATTTGGACACATTTACGGATAGATTACCTAACGCTGGAGAAACTTTCAGGGCTAACCACTTCGAAACACATGCTGGTGGTAAGGGATTGAACCAAGCTGCGGCCATTGGTAAATTAAAAAACCCCAGCAGCAGATATAGTGTTCGAATGATTGGTAATGTTGGAAATGATACATTTGGTAAACAATTGAAGGACACTTTATCCGATTGCGGAGTCGATATCACTCACGTCGGTACTTACGAAGGCATTAATACGGGTACCGCTACCATATTAATTGAAGAGAAAGCTGGTGGCCAAAATAGGATATTGATTGTAGAAGGTGCTAACAGCAAGACTATTTATGACCCGAAACAGTTGTGTGAAATTTTTCCAGAGGGCAAGGAGGAAGAAGAGTATGTTGTTTTTCAACACGAAATTCCTGATCCTCTTTCCATTATTAAATGGATACATGCGAACAGGCCGAATTTTCAGATCGTATATAACCCCTCACCTTTCAAGACCATGCCTAAGAAAGATTGGGAGTTGGTAGACCTTTTGGTCGTTAATGAAATTGAGGGTCTTCAAATCGTGGAAAGTGTATTTGATAATGAACTTGTTGAAGAAATAAGGGAGAAGATAAAGGACGACTTTTTAGGAGAATATCGTAAAATTTGTGAGCTTTTGTATGAAAAACTCATGAATCGAAAGAAAAGAGGAATTGTGGTTATGACTTTGGGTTCGAGAGGGGTGCTTTTCTGTTCGCACGAAAGCCCTGAAGTACAATTCCTTCCGGCTATTCAAAATGTTTCGGTTGTTGATACTACAGGAGCTGGAGATACTTTCCTGGGCGGTTTGGTTACTCAATTGTATCAAGGAGAGACCTTGTCTATGGCTATAAAGTTCTCTACATTAGCTAGTTCATTGACCATTCAAAGAAAAGGTGCTGCTGAAAGCATGCCACTGTATAAAGATGTTCAGAAAGATGCATAA","protein_sequence":"MGITVIGSLNYDLDTFTDRLPNAGETFRANHFETHAGGKGLNQAAAIGKLKNPSSRYSVRMIGNVGNDTFGKQLKDTLSDCGVDITHVGTYEGINTGTATILIEEKAGGQNRILIVEGANSKTIYDPKQLCEIFPEGKEEEEYVVFQHEIPDPLSIIKWIHANRPNFQIVYNPSPFKAMPKKDWELVDLLVVNEIEGLQIVESVFDNELVEEIREKIKDDFLGEYRKICELLYEKLMNRKKRGIVVMTLGSRGVLFCSHESPEVQFLPAIQNVSVVDTTGAGDTFLGGLVTQLYQGETLSTAIKFSTLASSLTIQRKGAAESMPLYKDVQKDA"}]}