{"ymdb_id":"YMDB00067","created_at":"2011-05-29T15:53:36.000Z","updated_at":"2016-09-08T18:34:58.000Z","name":"5-Phosphoribosylamine","cas":"14050-66-9","state":"Solid","melting_point":"","description":"5-Phosphoribosylamine is a substrate for amidophosphoribosyltransferase and trifunctional purine biosynthetic protein adenosine-3. It is an intermediate in purine metabolism and a precursor to IMP. It is generated from Phosphoribosyl pyrophosphate (PRPP). [Wikipedia]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":null,"chebi_id":"37737","hmdb_id":"HMDB01128","kegg_id":"C03090","pubchem_id":"150","cs_id":"388939","foodb_id":null,"wikipedia_link":"Phosphoribosylamine","biocyc_id":"5-P-BETA-D-RIBOSYL-AMINE","iupac":"{[(2R,3S,4R,5R)-5-amino-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"5-phospho-β-D-ribosylamine","logp":"-3.545345242649598","pka":"6.243630161593156","alogps_solubility":"3.82e+01 g/l","alogps_logp":"-2.39","alogps_logs":"-0.78","acceptor_count":"7","donor_count":"5","rotatable_bond_count":"3","polar_surface_area":"142.47","refractivity":"42.491299999999995","polarizability":"18.663161093312503","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"8.000221098750375","pka_strongest_acidic":"1.2256230940421675","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["5-P-beta-D-ribosyl-amine","5-P-beta-delta-ribosyl-amine","5-phospho-beta-D-ribosyl-amine","5-phospho-beta-D-ribosylamine","5-phospho-beta-delta-ribosyl-amine","5-phospho-beta-delta-ribosylamine","5-phospho-D-ribosylamine","5-phospho-delta-ribosylamine","5-phosphoribosylamine","PRA"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Alanine, aspartate and glutamate metabolism","kegg_map_id":"00250"},{"name":"purine nucleotides de novo biosynthesis","kegg_map_id":null}],"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."}],"proteins":[{"created_at":"2011-05-24T19:40:15.000Z","updated_at":"2011-05-27T14:55:58.000Z","name":"Amidophosphoribosyltransferase","uniprot_id":"P04046","uniprot_name":"PUR1_YEAST","enzyme":true,"transporter":false,"gene_name":"ADE4","num_residues":510,"molecular_weight":"56718.89844","theoretical_pi":"6.2","general_function":"Involved in amidophosphoribosyltransferase activity","specific_function":"5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O","reactions":[{"id":1578,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2263,"direction":"\u003e","locations":null,"altext":"5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"K02203","genbank_protein_id":"171009","gene_card_id":"ADE4","chromosome_location":"chromosome 13","locus":"YMR300C","synonyms":["ATase","Glutamine phosphoribosylpyrophosphate amidotransferase"],"enzyme_classes":["2.4.2.14"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Function","description":" amidophosphoribosyltransferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring glycosyl groups"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular aromatic compound metabolic process"},{"category":"Process","description":" nucleobase metabolic process"},{"category":"Process","description":" nucleoside metabolic process"},{"category":"Process","description":" purine base metabolic process"},{"category":"Process","description":" purine base biosynthetic process"},{"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"}],"pfams":[{"name":"GATase_2","identifier":"PF00310"},{"name":"Pribosyltran","identifier":"PF00156"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Alanine, aspartate and glutamate metabolism","kegg_map_id":"00250"}],"gene_sequence":"ATGTGTGGTATTTTAGGTATTGTATTAGCAAACCAAACCACTCCAGTAGCTCCGGAGTTATGTGATGGATGCATTTTTCTACAACATCGTGGACAAGATGCAGCTGGTATAGCTACCTGTGGTTCTCGTGGTAGAGTCTGCCAATGTAAAGGTAATGGTATGGCTCGTGACGTATTTACCCAACGTGTTTCCGGTCTTGCTGGTTCCATGGGTATTGCCCACTTGAGATATCCTACACCGGGTCTTCGGCTAATTCTAGAAGCGCAACCATTTTACGTCAATAGTCCTTACGGTATTAACTTGGCACATAACGGTAACTTGGTGAATACTGCATCATTGAAGAGATATATGGATGAAGACGTTCATAGACATATTAACACGGACAGTGATTCGGAGTTACTATTGAATATTTTTGCTGCTGAACTGGAAAAACATAACAAGTACAGAGTTAACAATGAAGATGGTTTCTCCAACGCGTTAGAAGGTGTTTACCGTTTATGCCGTGGCGGTTATGCTTGCGTTGGTTTACTTGCCGGTTTTGCATTATTTGGTTTCAGAGATCCAAATGGTATTAGGCCATTATTGTTCGGTGAAAGAGAAAATCCGGACGGCACTAAGGACTATATGTTAGCTTCAGAAAGTGTTGTTTTCAAAGCTCACAACTTTACTAAATATCGTGACTTAAAGCCTGGCGAGGCAGGTATCATCCCTAAGAACTGTAGCAAAGGTGAACCTGAGTTCAAACAAGTGGTTCCTATTAACTCTTATAGACCTGATTTATTTGAATACGTATATTTCGCCAGACCGGACAGTGTCTTGGATGGAATATCAGTTTATCACACAAGATTGGCTATGGGTTCTAAATTAGCGCAAAATATTCTAAAGCAACTGAAGCCAGAAGATATTGATGTTGTTATTCCCGTCCCAGATACTGCAAGAACATGTGCACTAGAATGTGCTAATGTGTTAGGTAAGCCTTATAGAGAGGGCTTTGTTAAAAACAGATACGTGGGCAGGACATTTATCATGCCAAACCAGAGGGAAAGGGTTTCTTCAGTAAGGAGGAAGCTTAACCCTATGGAGTCTGAATTTAAGGGTAAGAAGGTTCTGATAGTGGATGATTCTATTGTCAGAGGTACTACTTCAAAAGAGATTGTTAACATGGCCAAGGAATCCGGTGCAACAAAGGTTTACTTCGCTTCAGCTGCCCCAGCCATTCGTTACAACCATATTTATGGTATTGACTTAACAGACACAAAGAACTTGATTGCTTATAACAGAACCGATGAAGAAGTGGCGGAAGTAATCGGTTGTGAAAGAGTCATTTACCAATCATTGGAAGATTTGATTGATTGTTGTAAAACTGATAAAATAACCAAATTCGAAGATGGTGTATTTACCGGAAATTATGTCACTGGTGTTGAAGACGGTTATATTCAAGAATTGGAAGAAAAACGTGAATCGATCGCAAATAATTCATCAGATATGAAGGCTGAAGTCGATATCGGATTATATAATTGTGCAGATTATTGA","protein_sequence":"MCGILGIVLANQTTPVAPELCDGCIFLQHRGQDAAGIATCGSRGRIYQCKGNGMARDVFTQQRVSGLAGSMGIAHLRYPTAGSSANSEAQPFYVNSPYGINLAHNGNLVNTASLKRYMDEDVHRHINTDSDSELLLNIFAAELEKHNKYRVNNEDVFHALEGVYRLCRGGYACVGLLAGFALFGFRDPNGIRPLLFGERENPDGTKDYMLASESVVFKAHNFTKYRDLKPGEAVIIPKNCSKGEPEFKQVVPINSYRPDLFEYVYFARPDSVLDGISVYHTRLAMGSKLAENILKQLKPEDIDVVIPVPDTARTCALECANVLGKPYREGFVKNRYVGRTFIMPNQRERVSSVRRKLNPMESEFKGKKVLIVDDSIVRGTTSKEIVNMAKESGATKVYFASAAPAIRYNHIYGIDLTDTKNLIAYNRTDEEVAEVIGCERVIYQSLEDLIDCCKTDKITKFEDGVFTGNYVTGVEDGYIQELEEKRESIANNSSDMKAEVDIGLYNCADY"},{"created_at":"2011-05-24T20:12:36.000Z","updated_at":"2011-05-24T20:12:36.000Z","name":"Bifunctional purine biosynthetic protein ADE5,7","uniprot_id":"P07244","uniprot_name":"PUR2_YEAST","enzyme":true,"transporter":false,"gene_name":"ADE5","num_residues":802,"molecular_weight":"86067.39844","theoretical_pi":"4.89","general_function":"Involved in catalytic activity","specific_function":"ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide","reactions":[{"id":1885,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1891,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2304,"direction":"\u003e","locations":null,"altext":"ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.","export":false,"pw_reaction_id":null,"source":null},{"id":2305,"direction":"\u003e","locations":null,"altext":"ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X04337","genbank_protein_id":"3335","gene_card_id":"ADE5","chromosome_location":null,"locus":"YGL234W","synonyms":["Phosphoribosylamine--glycine ligase","Glycinamide ribonucleotide synthetase","GARS","Phosphoribosylglycinamide synthetase","Phosphoribosylformylglycinamidine cyclo-ligase","AIR synthase","AIRS","Phosphoribosyl-aminoimidazole synthetase"],"enzyme_classes":["6.3.4.13","6.3.3.1"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" cyclo-ligase activity"},{"category":"Function","description":" phosphoribosylformylglycinamidine cyclo-ligase activity"},{"category":"Function","description":" phosphoribosylamine-glycine ligase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" ligase activity"},{"category":"Function","description":" ligase activity, forming carbon-nitrogen bonds"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" cellular aromatic compound metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" nucleobase metabolic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" purine base metabolic process"},{"category":"Process","description":" purine nucleotide biosynthetic process"},{"category":"Process","description":" purine base biosynthetic process"},{"category":"Process","description":" purine nucleoside monophosphate biosynthetic process"},{"category":"Process","description":" purine ribonucleoside monophosphate biosynthetic process"},{"category":"Process","description":" IMP biosynthetic process"},{"category":"Process","description":" 'de novo' IMP biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"}],"pfams":[{"name":"AIRS","identifier":"PF00586"},{"name":"AIRS_C","identifier":"PF02769"},{"name":"GARS_A","identifier":"PF01071"},{"name":"GARS_C","identifier":"PF02843"},{"name":"GARS_N","identifier":"PF02844"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"gene_sequence":"ATGCTCAACATTCTCGTTTTAGGAAACGGTGCAAGAGAACACGTTCTTGTCACCAAGCTGGCTCAGTCACCCACCGTGGGTAAGATCTATGTCGCTCCAGGTAATGGAGGGACCGCAACCATGGATCCTTCGCGTGTGATAAACTGGGATATTACGCCAGATGTCGCCAATTTTGCTCGTTTGCAGTCGATGGCTGTGGAACATAAGATCAACTTGGTCGTTCCTGGTCCAGAATTACCTCTAGTCAACGGCATCACCTCCGTGTTCCATAGCGTTGGTATTCCCGTTTTTGGACCTTCCGTCAAAGCCGCTCAGTTGGAAGCTTCCAAGGCTTTCTCCAAGAGATTTATGTCAAAACACAATATTCCAACCGCGTCTTATGATGTCTTCACTAATCCAGAAGAAGCCATTTCATTCTTGCAAGCTCATACTGACAAAGCTTTTGTCATCAAGGCCGACGGGATCGCTGCTGGGAAAGGTGTTATTATCCCATCTAGCATCGACGAGTCCGTCCAAGCTATCAAGGACATAATGGTCACCAAGCAATTCGGTGAAGAAGCGGGCAAGCAGGTTGTGATAGAACAATTCTTGGAAGGTGATGAAATCTCTCTACTCACCATTGTTGACGGGTACTCTCACTTCAATCTCCCCGTCGCACAAGATCACAAGAGGATCTTTGATGGCGACAAGGGCTTGAACACCGGTGGGATGGGTGCCTATGCCCCCGCTCCTGTGGCCACACCATCTTTGTTGAAGACCATAGATTCACAGATTGTGAAGCCTACGATTGATGGGATGAGACGTGATGGTATGCCCTTTGTTGGTGTGCTGTTCACCGGGATGATTTTGGTGAAGGATTCTAAGACAAATCAACTTGTTCCCGAAGTGTTAGAATATAATGTCAGATTCGGTGACCCAGAGACACAGGCTGTTTTGAGTTTACTTGATGATCAAACCGATTTGGCGCAAGTGTTTTTGGCTGCTGCTGAACATCGTTTGGATTCCGTAAACATAGGAATCGATGACACAAGATCTGCCGTTACTGTCGTAGTGGCTGCAGGTGGTTATCCTGAATCATACGCCAAAGGTGACAAAATTACCTTGGATACCGATAAATTACCTCCACATACACAAATCTTCCAAGCAGGTACCAAATACGATTCCGCCACCGATTCTTTATTGACCAATGGTGGTAGAGTTCTTTCTGTGACCTCCACTGCTCAGGACTTGAGAACAGCAGTAGATACAGTATATGAAGCCGTCAAATGCGTCCATTTCCAAAATTCTTACTACAGAAAGGACATCGCATACCGTGCGTTCCAAAACTCAGAATCATCAAAAGTTGCCATCACATACGCAGACTCAGGTGTCTCTGTTGATAATGGTAACAATCTCGTACAAACTATCAAAGAAATGGTCAGATCCACAAGAAGGCCAGGTGCAGACTCTGATATTGGTGGTTTTGGTGGTTTATTCGATTTGGCTCAAGCAGGTTTCCGTCAAAACGAAGATACCTTACTAGTAGGTGCTACAGATGGTGTCGGTACTAAATTAATCATTGCCCAAGAGACCGGGATTCATAATACTGTCGGTATTGACCTGGTGGCCATGAATGTTAACGATTTGGTGGTACAAGGTGCTGAGCCTCTATTCTTTTTGGACTACTTTGCCACTGGTGCTCTTGACATTCAAGTTGCCTCTGATTTTGTGTCCGGTGTTGCTAATGGTTGTATTCAAAGTGGTTGTGCTCTTGTGGGTGGTGAAACTTCGGAAATGCCCGGTATGTATCCACCCGGCCACTACGATACTAATGGTACCGCTGTTGGTGCTGTATTAAGACAAGATATCTTGCCCAAGATAAATGAAATGGCCGCAGGAGATGTTCTTCTGGGTCTCGCCTCTAGCGGTGTTCATTCTAATGGTTTCTCTTTGGTTAGAAAAATTATTCAACATGTAGCATTACCATGGGACGCTCCATGTCCATGGGATGAATCTAAGACGTTAGGTGAAGGTATTCTTGAACCAACAAAAATTTACGTCAAGCAATTATTGCCATCAATTAGACAAAGACTACTACTAGGTTTAGCTCATATAACAGGTGGTGGTTTAGTAGAGAATATCCCAAGAGCTATTCCAGACCACCTACAGGCCCGCGTTGATATGTCAACCTGGGAAGTACCCCGTGTCTTCAAATGGTTTGGTCAAGCAGGTAATGTTCCACACGATGACATTTTAAGAACCTTCAACATGGGTGTTGGTATGGTTTTGATTGTCAAGAGAGAAAACGTCAAGGCTGTTTGTGATTCATTGACTGAAGAAGGTGAAATTATTTGGGAGCTTGGTTCTTTGCAAGAAAGACCAAAGGATGCTCCCGGTTGTGTGATTGAAAACGGAACTAAGCTTTACTAA","protein_sequence":"MLNILVLGNGAREHVLVTKLAQSPTVGKIYVAPGNGGTATMDPSRVINWDITPDVANFARLQSMAVEHKINLVVPGPELPLVNGITSVFHSVGIPVFGPSVKAAQLEASKAFSKRFMSKHNIPTASYDVFTNPEEAISFLQAHTDKAFVIKADGIAAGKGVIIPSSIDESVQAIKDIMVTKQFGEEAGKQVVIEQFLEGDEISLLTIVDGYSHFNLPVAQDHKRIFDGDKGLNTGGMGAYAPAPVATPSLLKTIDSQIVKPTIDGMRRDGMPFVGVLFTGMILVKDSKTNQLVPEVLEYNVRFGDPETQAVLSLLDDQTDLAQVFLAAAEHRLDSVNIGIDDTRSAVTVVVAAGGYPESYAKGDKITLDTDKLPPHTQIFQAGTKYDSATDSLLTNGGRVLSVTSTAQDLRTAVDTVYEAVKCVHFQNSYYRKDIAYRAFQNSESSKVAITYADSGVSVDNGNNLVQTIKEMVRSTRRPGADSDIGGFGGLFDLAQAGFRQNEDTLLVGATDGVGTKLIIAQETGIHNTVGIDLVAMNVNDLVVQGAEPLFFLDYFATGALDIQVASDFVSGVANGCIQSGCALVGGETSEMPGMYPPGHYDTNGTAVGAVLRQDILPKINEMAAGDVLLGLASSGVHSNGFSLVRKIIQHVALPWDAPCPWDESKTLGEGILEPTKIYVKQLLPSIRQRLLLGLAHITGGGLVENIPRAIPDHLQARVDMSTWEVPRVFKWFGQAGNVPHDDILRTFNMGVGMVLIVKRENVKAVCDSLTEEGEIIWELGSLQERPKDAPGCVIENGTKLY"}]}