{"ymdb_id":"YMDB00765","created_at":"2011-05-29T18:51:09.000Z","updated_at":"2016-09-08T18:35:52.000Z","name":"5-Amino-6-(D-ribitylamino)uracil","cas":null,"state":null,"melting_point":null,"description":"5-Amino-6-(D-ribitylamino)uracil is an intermediate in flavin biosynthesis pathway. Riboflavin (vitamin B2) is the precursor for the essential flavin cofactors FMN and FAD, which are used in a wide variety of redox reactions. [Biocyc PWY-6168]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":null,"chebi_id":"15934","hmdb_id":null,"kegg_id":"C04732","pubchem_id":"14056325","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"5-amino-6-{[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino}-1,2,3,4-tetrahydropyrimidine-2,4-dione","traditional_iupac":"5-arpd","logp":"-4.389022046999999","pka":"12.634784897543604","alogps_solubility":"1.43e+01 g/l","alogps_logp":"-2.44","alogps_logs":"-1.29","acceptor_count":"8","donor_count":"8","rotatable_bond_count":"6","polar_surface_area":"177.17","refractivity":"71.48459999999999","polarizability":"25.817806028191033","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.7435879201365787","pka_strongest_acidic":"8.47601881113622","bioavailability":"1","number_of_rings":"1","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine","5-amino-2,6-dioxo-4-ribitylaminopyrimidine","5-Amino-6-(1-D-ribitylamino)uracil","5-amino-6-(D-ribitylamino)uracil","5-amino-6-ribitylamino-2,4-(1H,3H)pyrimidinedione","5-Amino-6-ribitylaminouracil","5-arpd","6-(1-D-Ribitylamino)-5-amino-2,4-dihydroxypyrimidine","6-(1-D-Ribitylamino)-5-aminouracil"],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"},{"name":"Methane metabolism","kegg_map_id":"00680"}],"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":"2011-05-27T03:06:29.000Z","updated_at":"2011-05-27T15:01:19.000Z","name":"6,7-dimethyl-8-ribityllumazine synthase","uniprot_id":"P50861","uniprot_name":"RIB4_YEAST","enzyme":true,"transporter":false,"gene_name":"RIB4","num_residues":169,"molecular_weight":"18555.40039","theoretical_pi":"6.51","general_function":"Involved in riboflavin biosynthetic process","specific_function":"Condensation of 5-amino-6-(1'-D)-ribityl-amino- 2,4(1H,3H)-pyrimidinedione with L-3,4-dihydroxy-2-butanone 4- phosphate to produce 6,7-dimethyl-8-(1-D-ribityl)lumazine","reactions":[{"id":1942,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2705,"direction":"\u003e","locations":"","altext":"2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.","export":false,"pw_reaction_id":null,"source":null},{"id":14112,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006543","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1EJB","cellular_location":null,"genbank_gene_id":"AY558430","genbank_protein_id":"45270750","gene_card_id":"RIB4","chromosome_location":"chromosome 15","locus":"YOL143C","synonyms":["DMRL synthase","Lumazine synthase","Riboflavin synthase beta chain"],"enzyme_classes":["2.5.1.9"],"go_classes":[{"category":"Component","description":" riboflavin synthase complex"},{"category":"Component","description":" macromolecular complex"},{"category":"Component","description":" protein complex"},{"category":"Function","description":" Not Available"},{"category":"Process","description":" riboflavin biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" riboflavin metabolic process"}],"pfams":[{"name":"DMRL_synthase","identifier":"PF00885"}],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"gene_sequence":"ATGGCAGTTAAAGGATTAGGCAAACCAGATCAAGTTTATGACGGTTCCAAAATCAGGGTCGGTATCATTCATGCCCGTTGGAACCGTGTCATTATTGACGCTCTTGTGAAAGGTGCTATTGAAAGAATGGCTTCCCTTGGTGTCGAGGAAAATAACATAATAATTGAAACTGTTCCTGGATCCTATGAATTACCTTGGGGGACAAAAAGGTTTGTTGACAGACAAGCGAAGTTGGGAAAGCCGCTAGATGTTGTAATTCCTATTGGTGTACTTATCAAAGGTAGTACAATGCACTTTGAATACATTTCAGATTCCACCACTCACGCATTGATGAACTTACAAGAAAAAGTCGACATGCCCGTCATTTTTGGCCTCTTAACTTGCATGACTGAAGAACAAGCCCTGGCCAGAGCTGGCATCGATGAAGCGCACTCCATGCACAACCATGGTGAAGATTGGGGTGCTGCAGCAGTGGAAATGGCTGTTAAGTTCGGTAAAAATGCTTTTTGA","protein_sequence":"MAVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF"},{"created_at":"2011-05-27T03:07:11.000Z","updated_at":"2011-05-27T15:01:19.000Z","name":"Riboflavin synthase alpha chain","uniprot_id":"P38145","uniprot_name":"RISA_YEAST","enzyme":true,"transporter":false,"gene_name":"RIB5","num_residues":238,"molecular_weight":"26195.59961","theoretical_pi":"4.81","general_function":"Involved in riboflavin synthase activity","specific_function":"2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine","reactions":[{"id":1943,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2705,"direction":"\u003e","locations":"","altext":"2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.","export":false,"pw_reaction_id":null,"source":null},{"id":14113,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006544","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X70529","genbank_protein_id":"1907247","gene_card_id":"RIB5","chromosome_location":"chromosome 2","locus":"YBR256C","synonyms":[],"enzyme_classes":["2.5.1.9"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" riboflavin synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring alkyl or aryl (other than methyl) groups"},{"category":"Process","description":" riboflavin metabolic process"},{"category":"Process","description":" riboflavin biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"}],"pfams":[{"name":"Lum_binding","identifier":"PF00677"}],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"gene_sequence":"ATGTTTACTGGTATTGTAGAATGCATGGGGACTGTTTTGGAAAACAACCCATATGATGACTCTGAAAGTGGAGGTCAAGGAGTTTCTATTACTATTGGCAATGCGGGGAGTATTCTCACCGATTGTCACGTTGGAGATTCAATAGCCGTAAATGGGGTATGCCTTACTGTGACCGAGTTTAATAACGACTCCTTCAAAGTTGGGATATCACCAGAAACTATAAAACGAAGTAATGTCGCTTCCTGGATTCAAGGCACCCAGGTCAACTTGGAGAGAGCGGTATCTCAAGACGTTAGGTTCGGTGGTCATTATGTACAGGGTCACGTAGACACTGTTGCTAATATTGTCTCAAGAAGACCTGAGGGGAATTCAATTATTTTTGGGTTTCAGTTAAGAGATCAAGAGTACTTTAAATACATAGTAGAAAAGGGATTCATTTGTATAGATGGAACTTCCTTGACCATAATCAAGGTTGACCCACTTTCGCAAGGTGGAGCCTTCTATATTAGTATGATAAAGCACACCCAAGACAATGTTATCATGCCTTTGAAGAAAATTGGCGACGAGGTTAATATTGAAGTAGATTTGACTGGGAAGATTATTGAGAAGCAAATTCTATTAACGTTGGAAAACCAAATATCAAAGAAAGATAGTACTTTGAATACTATGATCTCAAACATTATCGAGGAGAAGGTTAGAAACTACCTAAATAAATAA","protein_sequence":"MFTGIVECMGTVLENNPYDDSESGGQGVSITIGNAGSILTDCHVGDSIAVNGVCLTVTEFNNDSFKVGISPETIKRSNVASWIQGTQVNLERAVSQDVRFGGHYVQGHVDTVANIVSRRPEGNSIIFGFQLRDQEYFKYIVEKGFICIDGTSLTIIKVDPLSQGGAFYISMIKHTQDNVIMPLKKIGDEVNIEVDLTGKIIEKQILLTLENQISKKDSTLNTMISNIIEEKVRNYLNK"}]}