{"ymdb_id":"YMDB00425","created_at":"2011-05-29T18:15:55.000Z","updated_at":"2016-09-08T18:35:28.000Z","name":"5-Amino-6-(5-phospho-D-ribitylamino)uracil","cas":null,"state":null,"melting_point":null,"description":"5-Amino-6-(5-phospho-D-ribitylamino)uracil is an intermediate in flavin biosynthesis pathway. [Biocyc RIBOSYN2-PWY]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"","synthesis_reference":null,"chebi_id":"18247","hmdb_id":null,"kegg_id":"C04454","pubchem_id":"45266638","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"{[(2R,3S,4S)-5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxy}phosphonic acid","traditional_iupac":"[(2R,3S,4S)-5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxyphosphonic acid","logp":"-4.512588078333334","pka":"6.513137596770021","alogps_solubility":"2.89e+00 g/l","alogps_logp":"-2.49","alogps_logs":"-2.09","acceptor_count":"10","donor_count":"9","rotatable_bond_count":"8","polar_surface_area":"223.7","refractivity":"82.35749999999999","polarizability":"30.06072185432768","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-2.743613426263205","pka_strongest_acidic":"1.4921085022698914","bioavailability":"0","number_of_rings":"1","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine","5-Amino-2,6-dioxy-4-(5'-phosphoribitylamino)pyrimidine","5-Amino-6-(5-phosphoribitylamino)uracil","5-Amino-6-(5'-phospho-D-ribitylamino)uracil","5-Amino-6-(5'-phosphoribitylamino)uracil"],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"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":9068650,"citation":"Richter, G., Fischer, M., Krieger, C., Eberhardt, S., Luttgen, H., Gerstenschlager, I., Bacher, A. (1997). \"Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis.\" J Bacteriol 179:2022-2028."}],"proteins":[{"created_at":"2011-05-26T18:16:28.000Z","updated_at":"2011-07-22T17:53:40.000Z","name":"Bifunctional protein RIB2","uniprot_id":"Q12362","uniprot_name":"RIB2_YEAST","enzyme":true,"transporter":false,"gene_name":"RIB2","num_residues":591,"molecular_weight":"67035.29688","theoretical_pi":"6.51","general_function":"Involved in zinc ion binding","specific_function":"Involved in riboflavin biosynthesis. Converts 2,5- diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5- amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate","reactions":[{"id":1137,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2520,"direction":"\u003e","locations":"Cytoplasm;Nucleus. Mitochondrion;Nucleus","altext":"tRNA uridine = tRNA pseudouridine.","export":false,"pw_reaction_id":null,"source":null},{"id":2521,"direction":"\u003e","locations":"Cytoplasm","altext":"2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3).","export":false,"pw_reaction_id":null,"source":null},{"id":14110,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006541","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"Z21618","genbank_protein_id":"642221","gene_card_id":"RIB2","chromosome_location":"chromosome 15","locus":"YOL066C","synonyms":["tRNA pseudouridine synthase 8, cytoplasmic","tRNA pseudouridylate synthase 8","tRNA-uridine isomerase 8","Diaminohydroxyphosphoribosylaminopyrimidine deaminase","DRAP deaminase","Riboflavin-specific deaminase"],"enzyme_classes":["5.4.99.-","3.5.4.26"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" transition metal ion binding"},{"category":"Function","description":" zinc ion binding"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" isomerase activity"},{"category":"Function","description":" intramolecular transferase activity"},{"category":"Function","description":" nucleic acid binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" pseudouridine synthase activity"},{"category":"Function","description":" RNA binding"},{"category":"Process","description":" macromolecule metabolic process"},{"category":"Process","description":" RNA modification"},{"category":"Process","description":" pseudouridine synthesis"},{"category":"Process","description":" cellular macromolecule metabolic process"},{"category":"Process","description":" RNA metabolic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"dCMP_cyt_deam_1","identifier":"PF00383"},{"name":"PseudoU_synth_2","identifier":"PF00849"}],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"gene_sequence":"ATGGAGGACTCTAATAATGAAGCCAGCGATGACTTCAACAACTTATTAAACAAAGAAATTGAGTCTGCAAAGGAAGTGAAGTTAAGAAAATTCGCGAACAGGAATAATAATAGGAACGAAAACAGTTCCAAAGTCAAAGATGCGAGTGGATTCAGACTGAGAGTTATTCAAACCGATGGGCACAAAACTAAAAAGACAGACCCTGATTATGAAGTGACAATTGATGGACCCTTAAGGAAGATTGAGCCTTATTTTTTCACTTATAAAACTTTCTGTAAGGAGAGGTGGAGAGATCGTAAGTTGGTGGATGTATTCGTGAGCGAATTCAGGGATCGAGAGCCCAGCTATTATTCCAAAACCATTGCAGAGGGAAAAGTATACTTAAACGATGAACCTGCAAACCTTGATACCATCATTCGTGACGGTGATCTGATCACACATAAAGTACATCGACATGAACCGCCAGTCACATCTAAACCAATAGATATTGTGTTTGAAGACGAAGATATCCTTGTCATTGATAAACCCAGCAGTATTCCAGTGCACCCAACGGGCAGATACAGATTCAATACCATTACAAAAATGCTAGAAAGACAGCTAGGTTATTCAGTACATCCATGTAATAGACTAGACAAGCCAACTAGTGGACTAATGTTTTTAGCCAAGACTCCATTAGGTGCAGATAGAATGGGAGACCAAATGAAAGCGAGGGAAGTCACCAAAGAATACGTAGCCCGCGTGAAGGGCGAGTTCCCTATAGGTATAGTAGAGGTAGATAAGCCTGTCAGATCTGTTAACCCTAAAGTTGCACTAAACGCTGTTTGCGAGATGAGCGATGAAAACGCTAAACATGCCAAGACCGTTTTCCAAAGGGTTAGCTATGATGGACAGACGAGTATTGTAAAGTGTAAACCATTGACAGGTAGAACTCACCAAATAAGAGTCCATTTGCAGTACTTGGGATTTCCCATAGCAAATGACCCTATATACTCGAACCCAGATATCTGGGGTCCAGATTTGGGCCGCGGTGGACTTCAAAACTATGATGACATCGTTCTGAAACTAGACGCTATTGGCAAGACTAATCCTGCAGAGAGCTGGATTCATCCTCATAGCGAGGGTGAATACTTGCTTGGCCGTCAGTGCGAAGAATGCGAGGCTGAAATGTACACAGATCCCGGTACTAATGATCTCGACCTCTGGCTGCATGCCTTCCGGTACGAGTCATTGGAAAGAAATTCGGATACGCAAAAACCTCTCTGGAGTTATAGAACAAAATACCCTGAATGGGCCTTAGAGCCACATCGCCGATATATGGAAATGGCCGTTAAGGAAGCTGGTAAGTGTGGCCCGACAAAGACTGCTTTTAGTGTTGGTGCCGTTCTTGTTCATGGAACTCAAGTACTTGCCACAGGATATTCAAGAGAGCTACCAGGAAACACTCATGCAGAACAGTGTGCTTTGATAAAGTACTCGCAGTTACACCCGAACTGTCCCACTATAGTCCCTATGGGAACAGTGCTCTATACAACCATGGAACCCTGTTCCTTCAGGCTAAGTGGCAATGAGCCTTGCTGCGATAGAATCCTGGCCACCCAAGGTGCCATTGGTACTGTCTTCGTGGGGGTTATGGAGCCCGATACATTTGTTAAAAACAATACAAGTTTGAACAAGCTGGAATCGCACGGTGTGAACTACATACAAATACCAGGCTACGAGGAGGAGTGCACCATCATTGCCTTCAAAGGCCACGATAATAGTGACGACAAAGCTTAG","protein_sequence":"MEDSNNEASDDFNNLLNKEIESAKEVKLRKFANRNNNRNENSSKVKDASGFRLRVIQTDGHKTKKTDPDYEVTIDGPLRKIEPYFFTYKTFCKERWRDRKLVDVFVSEFRDREPSYYSKTIAEGKVYLNDEPANLDTIIRDGDLITHKVHRHEPPVTSKPIDIVFEDEDILVIDKPSSIPVHPTGRYRFNTITKMLERQLGYSVHPCNRLDKPTSGLMFLAKTPLGADRMGDQMKAREVTKEYVARVKGEFPIGIVEVDKPVRSVNPKVALNAVCEMSDENAKHAKTVFQRVSYDGQTSIVKCKPLTGRTHQIRVHLQYLGFPIANDPIYSNPDIWGPDLGRGGLQNYDDIVLKLDAIGKTNPAESWIHPHSEGEYLLGRQCEECEAEMYTDPGTNDLDLWLHAFRYESLERNSDTQKPLWSYRTKYPEWALEPHRRYMEMAVKEAGKCGPTKTAFSVGAVLVHGTQVLATGYSRELPGNTHAEQCALIKYSQLHPNCPTIVPMGTVLYTTMEPCSFRLSGNEPCCDRILATQGAIGTVFVGVMEPDTFVKNNTSLNKLESHGVNYIQIPGYEEECTIIAFKGHDNSDDKA"}]}