{"ymdb_id":"YMDB00253","created_at":"2011-05-29T17:58:56.000Z","updated_at":"2016-09-08T18:35:14.000Z","name":"D-Ribose","cas":"50-69-1","state":"Solid","melting_point":"95 oC","description":"Ribose is a five-carbon sugar (aldopentose). Only the D-isomers are known to occur naturally. Ribose is a component of RNA. Once phosphorylated, ribose can become a subunit of ATP, NADH, and several other compounds that are critical to metabolism like the secondary messengers cAMP and cGMP. Ribose is related to deoxyribose, as found in DNA.","experimental_water_solubility":"","experimental_logp_hydrophobicity":"-2.32 [HANSCH,C ET AL. (1995)]","location":null,"synthesis_reference":"Park, Yong-Cheol; Choi, Jin-Ho; Bennett, George N.; Seo, Jin-Ho. Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene. Journal of Biotechnology  (2006),  121(4),  508-516. ","chebi_id":"47013","hmdb_id":"HMDB00283","kegg_id":"C00121","pubchem_id":"5779","cs_id":"5575","foodb_id":null,"wikipedia_link":"Ribose","biocyc_id":"CPD-560","iupac":"(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol","traditional_iupac":"D-ribofuranoside","logp":"-2.302204276","pka":"12.899514700313038","alogps_solubility":"1.07e+03 g/l","alogps_logp":"-2.65","alogps_logs":"0.85","acceptor_count":"5","donor_count":"4","rotatable_bond_count":"1","polar_surface_area":"90.15","refractivity":"29.9609","polarizability":"13.681345802838806","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.9811390578102284","pka_strongest_acidic":"11.30569577774193","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["Alpha-d-ribose","alpha-D-ribose-5","Alpha-delta-ribose","alpha-delta-ribose-5","D-(-)-ribose","D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde","d-Ribose","delta-(-)-ribose","delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde","delta-Ribose","Ribose"],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"},{"name":"NAD metabolism","kegg_map_id":null}],"growth_conditions":[],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."},{"pubmed_id":21062828,"citation":"Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). \"BRENDA, the enzyme information system in 2011.\" Nucleic Acids Res 39:D670-D676."},{"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."}],"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":" catalytic activity"},{"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":"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"},{"created_at":"2011-05-27T17:15:59.000Z","updated_at":"2011-07-22T17:53:59.000Z","name":"Uridine nucleosidase","uniprot_id":"Q04179","uniprot_name":"URH1_YEAST","enzyme":true,"transporter":false,"gene_name":"URH1","num_residues":340,"molecular_weight":"37960.0","theoretical_pi":"5.07","general_function":"Involved in hydrolase activity, hydrolyzing N-glycosyl compounds","specific_function":"Also acts on cytidine","reactions":[{"id":1269,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1609,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2835,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"Uridine + H(2)O = D-ribose + uracil.","export":false,"pw_reaction_id":null,"source":null},{"id":4195,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006494","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":null,"genbank_protein_id":null,"gene_card_id":"URH1","chromosome_location":"chromosome 4","locus":"YDR400W","synonyms":["Uridine ribohydrolase"],"enzyme_classes":["3.2.2.3"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on glycosyl bonds"},{"category":"Function","description":" hydrolase activity, hydrolyzing N-glycosyl compounds"},{"category":"Process","description":" Not Available"}],"pfams":[{"name":"IU_nuc_hydro","identifier":"PF01156"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"NAD metabolism","kegg_map_id":null}],"gene_sequence":"ATGACTGTTAGTAAAATACCCATATGGCTAGATTGTGATCCTGGTCATGATGATGCCATAGCCATTTTATTAGGCTGTTTCCATCCAGCTTTCAATCTTCTAGGAATCAGCACGTGTTTTGGTAACGCACCGCCAGAGAATACTGACTACAACGCCCGTTCTCTTTTGACTGCGATGGGCAAAGCACAAGCGATTCCAGTTTATAAAGGCGCACAGAGACCTTGGAAAAGGGAACCTCATTATGCTCCTGACATTCATGGTATATCAGGTTTAGACGGCACTTCTTTGCTACCTAAGCCAACATTTGAGGCAAGAACTGATAAAACGTATATTGAGGCCATTGAAGAGGCGATTCTAGCTAACAATGGAGAGATATCCTTTGTGTCTACTGGTGCACTTACCACATTAGCAACAGTTTTTAGGTGTAAACCATACCTAAAAAAATCTGTCAAATATATTAGCATTATGGGGGGTGGACTCCATGGTCTAGGAAACTGTAACCCAAATCTTTCTGCTGAATTCAACGTTTGGATTGATCCTGACGCAGCGAATTACATATTCCGTGATCCCGATGTAAAGGACAAATGTATAGTAGTTCCTCTAAATTTAACTCACAAGGCCATAGCTACTTACAAGGTTAACGAAATGATATACAACGAAAAGAATAACAGCAAGTTACGAGAATTGTTTTTGGAGCTTTTTCAATTTTTTGCTCATACCTACAAGGATATGCAAGGATTTGAATCGGGCCCACCTATACATGATCCGGTAGCTTTGATGCCGCTTTTGGAATTTTATGGGTGGGATCCATCGTCTGCGGTTGGATTTCGCTACAAGAGAATGGACATATCCTGCATTGATGATGTTTTCAACGAAAACTCAGGGAAAATTATCATTGAAAAAGAATATCCAAATGACAGTGATGTTGGTACAATAATTGGTCTCGATTTGAATATCCAGTACTTTTGGGATCAGATTTTTGAAGCATTAAATAGAGCAGACAAAATGTCAACGATTGGATAA","protein_sequence":"MTVSKIPIWLDCDPGHDDAIAILLGCFHPAFNLLGISTCFGNAPPENTDYNARSLLTAMGKAQAIPVYKGAQRPWKREPHYAPDIHGISGLDGTSLLPKPTFEARTDKTYIEAIEEAILANNGEISFVSTGALTTLATVFRCKPYLKKSVKYISIMGGGLHGLGNCNPNLSAEFNVWIDPDAANYIFRDPDVKDKCIVVPLNLTHKAIATYKVNEMIYNEKNNSKLRELFLELFQFFAHTYKDMQGFESGPPIHDPVALMPLLEFYGWDPSSAVGFRYKRMDISCIDDVFNENSGKIIIEKEYPNDSDVGTIIGLDLNIQYFWDQIFEALNRADKMSTIG"}]}