{"ymdb_id":"YMDB00885","created_at":"2011-05-29T19:01:18.000Z","updated_at":"2016-09-08T18:36:01.000Z","name":"Thymine","cas":"65-71-4","state":"Solid","melting_point":"320 oC","description":"Thymine is a pyrimidine nucleobase. Thymine is found in DNA and replaced with uracil in RNA. In DNA, thymine binds to adenine via two hydrogen bonds to assist in stabilizing the nucleic acid structures.","experimental_water_solubility":"3.82 mg/mL at 25 oC [YALKOWSKY,SH \u0026 DANNENFELSER,RM (1992)]","experimental_logp_hydrophobicity":"-0.62 [HANSCH,C ET AL. (1995)]","location":"extracellular;cytoplasm","synthesis_reference":"Zhang, Shi-Ying; Wu, Da-Jun; Zhang, Yan-Ping.  Synthesis of thymine.    Zhongguo Yiyao Gongye Zazhi  (1999),  30(7),  325.","chebi_id":"17821","hmdb_id":"HMDB00262","kegg_id":"C00178","pubchem_id":"1135","cs_id":"1103","foodb_id":null,"wikipedia_link":"Thymine","biocyc_id":"THYMINE","iupac":"5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione","traditional_iupac":"thymine","logp":"-0.45974051066666644","pka":"14.002512971014774","alogps_solubility":"1.08e+01 g/l","alogps_logp":"-0.99","alogps_logs":"-1.07","acceptor_count":"2","donor_count":"2","rotatable_bond_count":"0","polar_surface_area":"58.2","refractivity":"30.326400000000003","polarizability":"11.422204494643946","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-4.998777587344984","pka_strongest_acidic":"9.057944384019686","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2,4-Dihydroxy-5-methylpyrimidine","4-Hydroxy-5-methylpyrimidin-2(1H)-one","5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione","5-Methyl-2,4-dihydroxypyrimidine","5-Methyl-2,4(1H,3H)-pyrimidinedione","5-Methylpyrimidine-2,4-dione","5-Methyluracil","Thymine"],"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."},{"pubmed_id":9025296,"citation":"Eddy, A. A. (1997). \"Expulsion of uracil and thymine from the yeast Saccharomyces cerevisiae: contrasting responses to changes in the proton electrochemical gradient.\" Microbiology 143 ( Pt 1):219-229."}],"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, transferring glycosyl groups"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Function","description":" purine-nucleoside phosphorylase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase 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"}]}