{"ymdb_id":"YMDB16311","created_at":"2016-09-12T18:35:03.000Z","updated_at":"2016-10-17T22:34:44.000Z","name":"5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine ","cas":null,"state":null,"melting_point":null,"description":null,"experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":null,"chebi_id":null,"hmdb_id":null,"kegg_id":null,"pubchem_id":null,"cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"1-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)","traditional_iupac":"1-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)","logp":"-4.512588078333334","pka":"6.513137596770021","alogps_solubility":"8.43e+00 g/l","alogps_logp":"-1.35","alogps_logs":"-1.72","acceptor_count":"10","donor_count":"4","rotatable_bond_count":"8","polar_surface_area":"237.85","refractivity":"111.76499999999999","polarizability":"29.128050600210322","formal_charge":"-5","physiological_charge":"-2","pka_strongest_basic":"-2.743613426263204","pka_strongest_acidic":"1.4921085022698914","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":[],"pathways":[{"name":"Riboflavin metabolism","kegg_map_id":"00740"}],"growth_conditions":[],"references":[],"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"}]}