{"ymdb_id":"YMDB00147","created_at":"2011-05-29T16:01:32.000Z","updated_at":"2016-09-08T18:35:06.000Z","name":"2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine","cas":null,"state":null,"melting_point":null,"description":"2,5-Diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one 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":"cytoplasm","synthesis_reference":null,"chebi_id":"29114","hmdb_id":null,"kegg_id":"C01304","pubchem_id":"439480","cs_id":"388579","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"{[(2R,3S,4R,5R)-5-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"APy","logp":"-4.229207798436231","pka":"6.240036904309666","alogps_solubility":"5.70e+00 g/l","alogps_logp":"-2.25","alogps_logs":"-1.79","acceptor_count":"11","donor_count":"8","rotatable_bond_count":"5","polar_surface_area":"221.98","refractivity":"82.05649999999999","polarizability":"29.99048991004865","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"1.7093533470768942","pka_strongest_acidic":"1.052770410004614","bioavailability":"0","number_of_rings":"2","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2,5-Diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one","2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine","2,5-Diamino-6-hydroxy-4-(5'-phosphoribosylamino)-pyrimidine","N-(2,5-diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-beta-D-ribofuranosylamine"],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"growth_conditions":[],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."},{"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":" 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":" pseudouridine synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" RNA binding"},{"category":"Function","description":" binding"},{"category":"Process","description":" cellular macromolecule metabolic process"},{"category":"Process","description":" RNA metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" RNA modification"},{"category":"Process","description":" macromolecule metabolic process"},{"category":"Process","description":" pseudouridine synthesis"}],"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"},{"created_at":"2011-05-27T02:42:30.000Z","updated_at":"2011-05-27T15:01:18.000Z","name":"GTP cyclohydrolase-2","uniprot_id":"P38066","uniprot_name":"RIB1_YEAST","enzyme":true,"transporter":false,"gene_name":"RIB1","num_residues":345,"molecular_weight":"38331.60156","theoretical_pi":"6.29","general_function":"Involved in GTP cyclohydrolase II activity","specific_function":"Catalyzes the conversion of GTP to 2,5-diamino-6- ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate","reactions":[{"id":1617,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2688,"direction":"\u003e","locations":"Cytoplasmic","altext":"GTP + 3 H(2)O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14108,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006539","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasmic","genbank_gene_id":"X74738","genbank_protein_id":"511141","gene_card_id":"RIB1","chromosome_location":"chromosome 2","locus":"YBL033C","synonyms":["GTP cyclohydrolase II"],"enzyme_classes":["3.5.4.25"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines"},{"category":"Function","description":" cyclohydrolase activity"},{"category":"Function","description":" GTP cyclohydrolase activity"},{"category":"Function","description":" GTP cyclohydrolase II activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" hydrolase activity"},{"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":"GTP_cyclohydro2","identifier":"PF00925"}],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"gene_sequence":"ATGACCATAGATAACTACGACAACAGTAAACAGGATAGCAGCAAATACGAGGTTAGTGGTACGGGTGATGGCAGGAACGGCGATGGCGGCTTGCCTCTAGTACAATGTGTCGCAAGAGCTCGTATCCCAACCACACAGGGTCCGGATATCTTTTTACATCTTTACAGTAACAACAGGGACAACAAGGAACATCTAGCCATTGTGTTTGGTGAAGACATACGGTCGCGCTCGCTATTCCGTAGAAGACAGTGCGAGACGCAACAAGATAGAATGATCAGGGGCGCTTATATTGGCAAACTGTATCCCGGCAGAACTGTGGCAGACGAAGACGATAGACTCGGATTAGCTCTGGAGTTTGATGATAGTACAGGTGAGTTATTAGCTTCCAAAGCCACTACATGGGACGCCCATAACGACACGCTGGTACGGATCCATTCTGAATGTTACACCGGTGAAAACGCATGGAGCGCCCGTTGTGATTGTGGTGAACAATTCGATAGGGCCGGTAGGCTTATCGCTTGCGACCACGAACCCACAAGCAAGATCAAAGGTGGAAACGGCCATGGTGTTATCGTGTATCTAAGACAAGAGGGTCGTGGCATCGGGTTAGGTGAGAAACTCAAGGCCTACAACCTGCAAGACTTAGGTGCTGACACAGTGCAGGCCAACTTAATGCTGAAACATCCCGTGGATGCTAGGGACTTCTCGCTGGGTAAGGCTATTTTGCTGGATCTTGGCATCGGTAATGTCAGGCTGCTGACAAATAACCCGGAAAAGATAAAACAGGTAGATCATGCGCCTTACCTTAAGTGCGTTGAACGAGTGCCTATGGTACCCATACACTGGACAAACTCCAGTGAAGGCATAGACTCCAAGGAGATAGAAGGTTATCTCAGGACCAAGATAGAAAGAATGGGTCATTTACTAACGGAGCCTCTGAAACTTCATACAAACCCTCAACCTACTGAGACAAGTGAAGCCCAAAACCAAAACCGTATGAACTCTGCGTTGTCATCAACATCGACGCTGGCAATATAA","protein_sequence":"MTIDNYDNSKQDSSKYEVSGTGDGRNGDGGLPLVQCVARARIPTTQGPDIFLHLYSNNRDNKEHLAIVFGEDIRSRSLFRRRQCETQQDRMIRGAYIGKLYPGRTVADEDDRLGLALEFDDSTGELLASKATTWDAHNDTLVRIHSECYTGENAWSARCDCGEQFDRAGRLIACDHEPTSNIKGGNGHGVIVYLRQEGRGIGLGEKLKAYNLQDLGADTVQANLMLKHPVDARDFSLGKAILLDLGIGNVRLLTNNPEKIKQVDHAPYLKCVERVPMVPIHWTNSSEGIDSKEIEGYLRTKIERMGHLLTEPLKLHTNPQPTETSEAQNQNRMNSALSSTSTLAI"},{"created_at":"2011-05-27T02:42:59.000Z","updated_at":"2011-07-22T17:53:41.000Z","name":"5-amino-6-(5-phosphoribosylamino)uracil reductase","uniprot_id":"P33312","uniprot_name":"RIB7_YEAST","enzyme":true,"transporter":false,"gene_name":"RIB7","num_residues":244,"molecular_weight":"27116.0","theoretical_pi":"6.78","general_function":"Involved in 5-amino-6-(5-phosphoribosylamino)uracil reductase activity","specific_function":"5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + NADPH","reactions":[{"id":1138,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2689,"direction":"\u003e","locations":null,"altext":"5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":14109,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006540","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY557713","genbank_protein_id":"45269317","gene_card_id":"RIB7","chromosome_location":"chromosome 2","locus":"YBR153W","synonyms":["HTP reductase"],"enzyme_classes":["1.1.1.193"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" nucleotide binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" oxidoreductase activity, acting on CH-OH group of donors"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor"},{"category":"Function","description":" NADP or NADPH binding"},{"category":"Function","description":" 5-amino-6-(5-phosphoribosylamino)uracil reductase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"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":"RibD_C","identifier":"PF01872"}],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"gene_sequence":"ATGTCTTTGACACCACTGTGTGAAGATTTACCACAATTTCTGCAAAACTATCTACCGAATGCTGGTCAAACGGAAAATACCATTGTGCCCTTTGTCACACTAACTTATGCTCAATCGCTCGACGCGAGAGTATCTAGGGGCCCTGGAGTGAGGACTACAATTTCACATCCCGAGACCAAAACAATGACGCATTATTTGAGACATCATCACGATGGAATACTCGTAGGAAGTGGAACAGTGCTAGCTGATAATCCTGGATTGAATTGTAAATGGGGTCCCGATCCGGCTGCAAATTCCCCAAGGCCAATAATAATAGATACAAAGCAAAAGTGGCGATTTGATGGTTCAAAAATGCAAGAACTTTTTATTAAACGACAGGGTAAGCCGCCAATCGTTGTTGTCACAAGTGAGCCCATTATAAAAGAACAACATGTAGACTACGCAATTTGTCCAATAAATGATACTACGAAATTGGTCGATTGGAAGAAATTGTTTGAGATATTAAAAGAAGAATTCAATATAAGGTCAGTAATGGTTGAAGGAGGTGCCAATGTAATAAATCAGTTGTTGCTGAGGAGCGATATTGTCAACAGTCTTATAATAACTATTGGATCAACATTTCTGGGTAGCTCAGGCACCGAAGTTAGCCCACCCCAAACAGTAAATTTAAAGGATATGTCATGGTGGAAGGGCATTACCGATGTGGTGCTTTGTGCGAGACTGGCCGATGACTAA","protein_sequence":"MSLTPLCEDLPQFLQNYLPNAGQTENTIVPFVTLTYAQSLDARVSRGPGVRTTISHPETKTMTHYLRHHHDGILVGSGTVLADNPGLNCKWGPDPAANSPRPIIIDTKQKWRFDGSKMQELFIKRQGKPPIVVVTSEPIIKEQHVDYAICPINDTTKLVDWKKLFEILKEEFNIRSVMVEGGANVINQLLLRSDIVNSLIITIGSTFLGSSGTEVSPPQTVNLKDMSWWKGITDVVLCARLADD"}]}