{"ymdb_id":"YMDB00662","created_at":"2011-05-29T18:41:24.000Z","updated_at":"2016-09-08T18:35:45.000Z","name":"2-deoxy-D-ribose 5-phosphate","cas":"102916-66-5","state":"Solid","melting_point":null,"description":"2-Deoxy-D-ribose 5-phosphate is an intermediate in purine deoxyribonucleosides degradation and pyrimidine deoxyribonucleosides degradation pathways. [Biocyc PWY0-1297 and PWY0-1298]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":"Method of preparing 2-deoxyribose 5-phosphate US Patent #7270992","chebi_id":"16132","hmdb_id":"HMDB01031","kegg_id":"C00673","pubchem_id":"635","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":"DEOXY-RIBOSE-5P","iupac":"{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"deoxyribose-5-phosphate","logp":"-1.5251322443333333","pka":"6.255762605408527","alogps_solubility":"3.75e+01 g/l","alogps_logp":"-2.14","alogps_logs":"-0.76","acceptor_count":"6","donor_count":"4","rotatable_bond_count":"3","polar_surface_area":"116.45000000000002","refractivity":"39.3231","polarizability":"17.46469128826616","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.2560418070675405","pka_strongest_acidic":"1.2299449119892785","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2-deoxy-5-O-phosphono-D-erythro-pentose","2-deoxy-alpha-D-ribose 5-phosphate","2-deoxy-alpha-delta-ribose 5-phosphate","2-Deoxy-D-ribose 5-phosphate","2-deoxy-d-ribose-5-phosphate","2-deoxyribose 5-phosphate","2-deoxyribose-5-p","2-deoxyribose-5-phosphate","deoxy-ribose-5p","Deoxyribose 5-phosphate","Deoxyribose 5-phosphic acid","deoxyribose-5-p","deoxyribose-5-phosphate"],"pathways":[{"name":"Pentose phosphate pathway","kegg_map_id":"00030"}],"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."}],"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. 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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"}]}