{"ymdb_id":"YMDB00760","created_at":"2011-05-29T18:50:43.000Z","updated_at":"2016-09-08T18:35:52.000Z","name":"N(1)-(5-phospho-D-ribosyl)glycinamide","cas":"10074-18-7","state":"Solid","melting_point":null,"description":"N(1)-(5-Phospho-D-ribosyl)glycinamide (glycineamideribotide) is an intermediate in purine metabolism. [Biocyc PWY-6277]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"Cytoplasm","synthesis_reference":null,"chebi_id":"18349","hmdb_id":"HMDB02022","kegg_id":"C03838","pubchem_id":"45266651","cs_id":"4573646","foodb_id":null,"wikipedia_link":null,"biocyc_id":"5-PHOSPHO-RIBOSYL-GLYCINEAMIDE","iupac":"{[(2R,3S,4R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"5'-phosphoribosylglycinamide","logp":"-4.650616976017662","pka":"6.245768050847792","alogps_solubility":"1.46e+01 g/l","alogps_logp":"-2.40","alogps_logs":"-1.29","acceptor_count":"8","donor_count":"6","rotatable_bond_count":"5","polar_surface_area":"171.57000000000002","refractivity":"55.294799999999995","polarizability":"23.69389940696378","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"8.141960108603826","pka_strongest_acidic":"1.2255744528280514","bioavailability":"1","number_of_rings":"1","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["5-phosphoribosylglycinamide","5'-Phosphoribosyl-glycineamide","5'-Phosphoribosylglycinamide","5'-Phosphoribosylglycineamide","GAR","gar, glycinamide ribonucleotide","Glycinamide ribonucleotide","Glycineamide ribonucleotide","Glycineamideribotide","N-glycyl-5-O-phosphono-D-ribofuranosylamine","N1-(5-phospho-D-ribosyl)glycinamide"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"One Carbon Pool by Folate I","kegg_map_id":null}],"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":15375647,"citation":"Yow, G. Y., Uo, T., Yoshimura, T., Esaki, N. (2004). \"D-amino acid N-acetyltransferase of Saccharomyces cerevisiae: a close homologue of histone acetyltransferase Hpa2p acting exclusively on free D-amino acids.\" Arch Microbiol 182:396-403."}],"proteins":[{"created_at":"2011-05-24T19:22:02.000Z","updated_at":"2011-05-27T14:55:57.000Z","name":"Phosphoribosylglycinamide formyltransferase","uniprot_id":"P04161","uniprot_name":"PUR3_YEAST","enzyme":true,"transporter":false,"gene_name":"ADE8","num_residues":214,"molecular_weight":"23540.0","theoretical_pi":"6.39","general_function":"Involved in hydroxymethyl-, formyl- and related transferase activity","specific_function":"10-formyltetrahydrofolate + N(1)-(5-phospho-D- ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5- phospho-D-ribosyl)glycinamide","reactions":[{"id":1890,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2249,"direction":"\u003e","locations":null,"altext":"10-formyltetrahydrofolate + N(1)-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide.","export":false,"pw_reaction_id":null,"source":null},{"id":4151,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006449","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"M36585","genbank_protein_id":"171015","gene_card_id":"ADE8","chromosome_location":"chromosome 4","locus":"YDR408C","synonyms":["5'-phosphoribosylglycinamide transformylase","GAR transformylase","GART"],"enzyme_classes":["2.1.2.2"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" methyltransferase activity"},{"category":"Function","description":" glycine hydroxymethyltransferase activity"},{"category":"Function","description":" hydroxymethyl-, formyl- and related transferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" phosphoribosylglycinamide formyltransferase activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring one-carbon groups"},{"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"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" purine nucleotide 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"}],"pfams":[{"name":"Formyl_trans_N","identifier":"PF00551"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"One carbon pool by folate","kegg_map_id":"00670"},{"name":"tetrahydrofolate biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGGCCAGAATTGTCGTATTAATTTCGGGCTCAGGTTCCAACTTGCAAGCCTTGATCGATGCCCAAAAGCAGGGCCAATTAGGCGAGGATGCTCATATTGTCTCTGTCATATCTTCCAGCAAGAAGGCATACGGGTTAACTAGGGCAGCGGACAATAATATCCCCACAAAGGTTTGTTCGCTATACCCATATACAAAGGGTATTGCGAAGGAGGACAAAGCCGCAAGGGCCAAGGCAAGATCCCAGTTTGAGAACGACCTCGCAAAACTAGTGCTCGAGGAAAAGCCTGACGTTATCATCTGCGCGGGCTGGTTATTGATCCTTGGATCTACTTTCTTGAGCCAACTGCAATCTGTGCCGATATTAAATCTGCATCCAGCGCTACCAGGTTGTTTCGATGGTACCACACACGCAATTGAAATGGCATGGCGCAAATGTCAGGACGAGAACAAGCCTCTGACGGCCGGATGCATGGTGCACTATGTCATCGAGGAGGTCGACAAGGGTGAGCCATTGGTGGTAAAAAAGCTAGAAATCATACCTGGCGAAGAAACACTAGAGCAGTACGAGCAAAGGGTACACGATGCTGAGCACATCGCGATTGTAGAAGCTACATATAAGGTTTTACAGCAGCTTCACAAATAA","protein_sequence":"MARIVVLISGSGSNLQALIDAQKQGQLGEDAHIVSVISSSKKAYGLTRAADNNIPTKVCSLYPYTKGIAKEDKAARAKARSQFENDLAKLVLEEKPDVIICAGWLLILGSTFLSQLQSVPILNLHPALPGCFDGTTHAIEMAWRKCQDENKPLTAGCMVHYVIEEVDKGEPLVVKKLEIIPGEETLEQYEQRVHDAEHIAIVEATYKVLQQLHK"},{"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":" 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":"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":" catalytic activity"},{"category":"Function","description":" phosphoribosylamine-glycine ligase activity"},{"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"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" cellular aromatic compound metabolic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" nucleobase metabolic process"},{"category":"Process","description":" purine nucleotide biosynthetic process"},{"category":"Process","description":" purine base metabolic process"},{"category":"Process","description":" purine nucleoside monophosphate biosynthetic process"},{"category":"Process","description":" purine base 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"}],"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"}]}