{"ymdb_id":"YMDB00507","created_at":"2011-05-29T18:24:46.000Z","updated_at":"2016-09-08T18:35:33.000Z","name":"Thymidine","cas":"50-89-5","state":"Solid","melting_point":"186.5 oC","description":"Thymidine (more precisely called 2'-deoxythymidine) is a pyrimidine deoxynucleoside. It is formed by a molecule of thymidine attached to a deoxyribose sugar molecule. Deoxythymidine is the DNA deoxynucleoside T.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":"-0.93 [SANGSTER (1993)]","location":"extracellular;cytoplasm","synthesis_reference":"Herdewijn, P.; Kerremans, L.; Wigerinck, P.; Vandendriessche, F.; Van Aerschot, A.  Synthesis of thymidine from 5-iodo-2'-deoxyuridine.    Tetrahedron Letters  (1991),  32(34),  4397-400.","chebi_id":"17748","hmdb_id":"HMDB00273","kegg_id":"C00214","pubchem_id":"5789","cs_id":"23630337","foodb_id":null,"wikipedia_link":"Thymidine","biocyc_id":"THYMIDINE","iupac":"1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione","traditional_iupac":"thymidine","logp":"-1.1190535893333329","pka":"13.907922676786033","alogps_solubility":"6.68e+01 g/l","alogps_logp":"-1.32","alogps_logs":"-0.56","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"99.1","refractivity":"55.412000000000006","polarizability":"23.060984366910677","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.9780835894464888","pka_strongest_acidic":"9.960276156373078","bioavailability":"1","number_of_rings":"2","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione","2-deoxythymidine","2-Desoxy-thymidine","2'-deoxy-5-methyl-Uridine","2'-deoxy-5-methyluridine","2'-Deoxythymidine","2'-thymidine","5-Methyl-2'-deoxyuridine","5-Methyldeoxyuridine","5-Methyldeoxyurindine","beta-D-Ribofuranoside, thymine-1 2-deoxy-","deoxyribosylthymine","Deoxyribothymidine","Deoxythymidin","deoxythymidine","Desoxy-thymidin","dT","dThd","DThyd","Thymidin","Thymidine","Thymidine, 2'-deoxy-","Thymine 2-desoxyriboside","thymine 2'-deoxyriboside","Thymine deoxyriboside","thymine-1 2-deoxy-b-D-Ribofuranoside","thymine-1 2-deoxy-beta-delta-Ribofuranoside","Thymine-2-deoxyriboside","Thymine-2-Desoxyriboside","Thyminedeoxyriboside","Uridine, 2'-deoxy-5-methyl-"],"pathways":[{"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."}],"proteins":[{"created_at":"2011-05-24T20:49:32.000Z","updated_at":"2011-07-22T17:54:36.000Z","name":"Purine nucleoside phosphorylase","uniprot_id":"Q05788","uniprot_name":"PNPH_YEAST","enzyme":true,"transporter":false,"gene_name":"PNP1","num_residues":311,"molecular_weight":"33754.60156","theoretical_pi":"7.31","general_function":"Involved in purine-nucleoside phosphorylase activity","specific_function":"Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules","reactions":[{"id":1447,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1915,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1916,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1917,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1918,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1919,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1920,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1921,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2012,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2349,"direction":"\u003e","locations":null,"altext":"Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY557950","genbank_protein_id":"45269792","gene_card_id":"PNP1","chromosome_location":"chromosome 12","locus":"YLR209C","synonyms":["PNP","Inosine phosphorylase"],"enzyme_classes":["2.4.2.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring glycosyl groups"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Function","description":" purine-nucleoside phosphorylase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside metabolic process"}],"pfams":[{"name":"PNP_UDP_1","identifier":"PF01048"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"Nicotinate and nicotinamide metabolism","kegg_map_id":"00760"}],"gene_sequence":"ATGAGTGATATCTTGAACGTAAGTCAACAACGTGAAGCAATTACCAAGGCCGCTGCGTATATTTCTGCTATTTTAGAACCACATTTCAAAAATACAACAAATTTCGAGCCTCCGAGAACTTTGATTATATGTGGTTCAGGGCTTGGTGGAATATCTACCAAGCTGTCTAGAGACAATCCACCCCCGGTAACAGTCCCATACCAAGACATCCCAGGATTCAAGAAAAGTACGGTTCCAGGTCATTCCGGTACACTAATGTTCGGATCTATGAATGGTTCACCAGTAGTATTAATGAATGGTCGTCTTCATGGATATGAAGGCAACACATTGTTTGAGACTACTTTTCCTATTAGAGTGCTTAACCACATGGGTCATGTTCGTAATTTAATTGTCACTAATGCCGCTGGTGGTATAAACGCGAAATATCAAGCCTGCGATTTGATGTGCATTTATGATCATTTAAATATCCCTGGCCTTGCTGGCCAGCACCCATTGAGAGGTCCTAACTTGGATGAAGATGGACCTCGTTTTTTAGCCTTGAGTGATGCATATGATCTGGAGTTGAGGAAGCTTTTATTTAAGAAATGGAAAGAGCTCAAGATTCAAAGGCCACTGCATGAAGGTACTTATACTTTTGTATCTGGACCCACTTTCGAAACAAGAGCAGAATCCAAAATGATAAGGATGTTGGGAGGAGATGCTGTCGGAATGAGTACTGTTCCCGAAGTCATTGTTGCAAGACATTGCGGATGGAGGGTTTTGGCCTTAAGTTTGATTACCAATACTTGCGTGGTGGATAGCCCTGCCAGTGCGTTGGACGAATCACCTGTACCCTTAGAAAAAGGCAAAGCGACTCACGCTGAAGTACTGGAGAATGGTAAAATCGCCTCTAATGACGTGCAAAACTTAATTGCTGCCGTAATGGGGGAATTATAA","protein_sequence":"MSDILNVSQQREAITKAAAYISAILEPHFKNTTNFEPPRTLIICGSGLGGISTKLSRDNPPPVTVPYQDIPGFKKSTVPGHSGTLMFGSMNGSPVVLMNGRLHGYEGNTLFETTFPIRVLNHMGHVRNLIVTNAAGGINAKYQACDLMCIYDHLNIPGLAGQHPLRGPNLDEDGPRFLALSDAYDLELRKLLFKKWKELKIQRPLHEGTYTFVSGPTFETRAESKMIRMLGGDAVGMSTVPEVIVARHCGWRVLALSLITNTCVVDSPASALDESPVPLEKGKATHAEVLENGKIASNDVQNLIAAVMGEL"}]}