{"ymdb_id":"YMDB00868","created_at":"2011-05-29T18:59:44.000Z","updated_at":"2016-09-08T18:36:00.000Z","name":"1-(5-phosphoribosyl)-5'-AMP","cas":null,"state":null,"melting_point":null,"description":"1-(5-Phosphoribosyl)-5'-AMP is an intermediate involved in histidine metabolism. [KEGG]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":null,"chebi_id":"18374","hmdb_id":null,"kegg_id":"C02741","pubchem_id":"11988267","cs_id":"24808237","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"{[(2R,3S,4R,5R)-5-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-6-imino-6,9-dihydro-1H-purin-9-yl}-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"Phosphoribosyl-AMP","logp":"-4.248617688907279","pka":"1.1481562688829214","alogps_solubility":"6.38e+00 g/l","alogps_logp":"-2.17","alogps_logs":"-1.94","acceptor_count":"16","donor_count":"9","rotatable_bond_count":"8","polar_surface_area":"290.17","refractivity":"122.5439","polarizability":"45.39895987684972","formal_charge":"0","physiological_charge":"-4","pka_strongest_basic":"5.949904897345005","pka_strongest_acidic":"0.6471132589828303","bioavailability":"0","number_of_rings":"4","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["1-(5-Phosphoribosyl)-AMP","5-phosphoribosyl-AMP","N1-(5-Phospho-D-ribosyl)-AMP","Phosphoribosyl-AMP"],"pathways":[{"name":"Histidine metabolism","kegg_map_id":"00340"},{"name":"Histidine Biosynthesis","kegg_map_id":null}],"growth_conditions":[],"references":[{"pubmed_id":21062828,"citation":"Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). \"BRENDA, the enzyme information system in 2011.\" Nucleic Acids Res 39:D670-D676."},{"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":379004,"citation":"Keesey, J. K. Jr, Bigelis, R., Fink, G. R. (1979). \"The product of the his4 gene cluster in Saccharomyces cerevisiae. A trifunctional polypeptide.\" J Biol Chem 254:7427-7433."}],"proteins":[{"created_at":"2011-05-26T21:40:20.000Z","updated_at":"2011-07-22T17:54:14.000Z","name":"ATP phosphoribosyltransferase","uniprot_id":"P00498","uniprot_name":"HIS1_YEAST","enzyme":true,"transporter":false,"gene_name":"HIS1","num_residues":297,"molecular_weight":"32266.09961","theoretical_pi":"5.94","general_function":"Involved in ATP phosphoribosyltransferase activity","specific_function":"Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of the enzymatic activity","reactions":[{"id":1342,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2612,"direction":"\u003e","locations":"Cytoplasm","altext":"1-(5-phospho-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":4153,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006451","source":"Smpdb"},{"id":4154,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006454","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"U18813","genbank_protein_id":"603291","gene_card_id":"HIS1","chromosome_location":"chromosome 5","locus":"YER055C","synonyms":["ATP-PRT","ATP-PRTase"],"enzyme_classes":["2.4.2.17"],"go_classes":[{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Component","description":" cell part"},{"category":"Function","description":" binding"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" transferase activity, transferring glycosyl groups"},{"category":"Function","description":" magnesium ion binding"},{"category":"Function","description":" ATP phosphoribosyltransferase activity"},{"category":"Process","description":" cellular amino acid metabolic process"},{"category":"Process","description":" histidine family amino acid metabolic process"},{"category":"Process","description":" histidine metabolic process"},{"category":"Process","description":" histidine biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"}],"pfams":[{"name":"HisG","identifier":"PF01634"},{"name":"HisG_C","identifier":"PF08029"}],"pathways":[{"name":"Histidine metabolism","kegg_map_id":"00340"},{"name":"Histidine Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGGATTTGGTGAACCATCTAACCGATAGACTACTGTTTGCAATCCCAAAGAAAGGTCGTTTATATTCTAAAAGTGTTTCTATTTTGAATGGTGCTGATATTACCTTTCACCGCTCTCAAAGATTAGACATTGCACTAAGCACAAGCTTACCTGTAGCGTTGGTCTTTCTGCCCGCTGCAGATATTCCAACTTTTGTTGGTGAAGGTAAATGTGATCTTGGTATAACTGGTGTTGACCAAGTTCGTGAATCTAACGTCGACGTAGACTTAGCAATCGATTTGCAATTTGGTAACTGTAAATTGCAGGTACAAGTCCCCGTAAATGGCGAGTATAAAAAGCCAGAACAGTTAATTGGCAAAACCATTGTTACCAGTTTCGTGAAACTTGCTGAAAAATACTTTGCCGATTTGGAAGGTACTACTGTTGAAAAAATGACCACAAGGATAAAGTTTGTCAGTGGTTCCGTGGAGGCATCATGTGCTCTGGGAATTGGTGATGCTATTGTAGATCTTGTAGAGAGTGGTGAGACAATGAGGGCAGCAGGTTTAGTTGATATTGCCACCGTCCTAAGCACAAGTGCCTACCTAATAGAATCAAAGAACCCAAAGAGCGATAAGAGTTTGATTGCTACTATCAAATCAAGAATTGAAGGTGTCATGACCGCTCAAAGGTTCGTTTCATGTATTTATAACGCACCTGAAGACAAGCTGCCTGAACTGTTGAAGGTGACGCCTGGCCGTAGAGCACCAACCATTTCCAAAATTGACGATGAAGGATGGGTTGCTGTTAGTTCCATGATTGAGAGAAAAACGAAGGGTGTTGTTTTAGATGAATTGAAAAGACTCGGCGCATCTGATATCATGGTTTTCGAAATTTCTAATTGTCGTGTATAA","protein_sequence":"MDLVNHLTDRLLFAIPKKGRLYSKSVSILNGADITFHRSQRLDIALSTSLPVALVFLPAADIPTFVGEGKCDLGITGVDQVRESNVDVDLAIDLQFGNCKLQVQVPVNGEYKKPEQLIGKTIVTSFVKLAEKYFADLEGTTVEKMTTRIKFVSGSVEASCALGIGDAIVDLVESGETMRAAGLVDIATVLSTSAYLIESKNPKSDKSLIATIKSRIEGVMTAQRFVSCIYNAPEDKLPELLKVTPGRRAPTISKIDDEGWVAVSSMIERKTKGVVLDELKRLGASDIMVFEISNCRV"},{"created_at":"2011-05-27T01:43:05.000Z","updated_at":"2011-05-27T15:01:15.000Z","name":"Histidine biosynthesis trifunctional protein","uniprot_id":"P00815","uniprot_name":"HIS2_YEAST","enzyme":true,"transporter":false,"gene_name":"HIS4","num_residues":799,"molecular_weight":"87720.5","theoretical_pi":"4.94","general_function":"Involved in oxidoreductase activity","specific_function":"1-(5-phosphoribosyl)-AMP + H(2)O = 1-(5- phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4-carboxamide","reactions":[{"id":1630,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1882,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1883,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2637,"direction":"\u003e","locations":"Cytoplasmic","altext":"1-(5-phosphoribosyl)-AMP + H(2)O = 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide.","export":false,"pw_reaction_id":null,"source":null},{"id":2638,"direction":"\u003e","locations":"Cytoplasmic","altext":"1-(5-phosphoribosyl)-ATP + H(2)O = 1-(5-phosphoribosyl)-AMP + diphosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":2639,"direction":"\u003e","locations":"Cytoplasmic","altext":"L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":4155,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006452","source":"Smpdb"},{"id":4156,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006453","source":"Smpdb"},{"id":4157,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006455","source":"Smpdb"},{"id":4158,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006461","source":"Smpdb"},{"id":4159,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006462","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasmic","genbank_gene_id":"V01310","genbank_protein_id":"3785","gene_card_id":"HIS4","chromosome_location":"chromosome 3","locus":"YCL030C","synonyms":["Phosphoribosyl-AMP cyclohydrolase","Phosphoribosyl-ATP pyrophosphohydrolase","Histidinol dehydrogenase","HDH"],"enzyme_classes":["3.5.4.19","3.6.1.31","1.1.1.23"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" nucleotide binding"},{"category":"Function","description":" NAD or NADH binding"},{"category":"Function","description":" hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines"},{"category":"Function","description":" cyclohydrolase activity"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" pyrophosphatase activity"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" phosphoribosyl-ATP diphosphatase activity"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" phosphoribosyl-AMP cyclohydrolase activity"},{"category":"Function","description":" transition metal ion binding"},{"category":"Function","description":" histidinol dehydrogenase activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" zinc ion binding"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"},{"category":"Function","description":" oxidoreductase activity, acting on CH-OH group of donors"},{"category":"Function","description":" hydrolase activity, acting on acid anhydrides"},{"category":"Function","description":" binding"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor"},{"category":"Process","description":" histidine family amino acid metabolic process"},{"category":"Process","description":" histidine metabolic process"},{"category":"Process","description":" histidine biosynthetic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"}],"pfams":[{"name":"Histidinol_dh","identifier":"PF00815"},{"name":"PRA-CH","identifier":"PF01502"},{"name":"PRA-PH","identifier":"PF01503"}],"pathways":[{"name":"Histidine metabolism","kegg_map_id":"00340"},{"name":"Histidine Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGGTTTTGCCGATTCTACCGTTAATTGATGATCTGGCCTCATGGAATAGTAAGAAGGAATACGTTTCACTTGTTGGTCAGGTACTTTTGGATGGCTCGAGCCTGAGTAATGAAGAGATTCTCCAGTTCTCCAAAGAGGAAGAAGTTCCATTGGTGCGTTTGTCCTTGCCAAGTGGTAAATTCAGCGATGATGAAATCATTGCCTTCTTGAACAACGGAGTTTCTTCTCTGTTCATTGCTAGCCAAGATGCTAAAACAGCCGAACACTTGGTTGAACAATTGAATGTACCAAAGGAGCGTGTTGTTGTGGAAGAGAACGGTGTTTTCTCCAATCAATTCATGGTAAAACAAAAATTCTCGCAAGATAAAATTGTGTCCATAAAGAAATTAAGCAAGGATATGTTGACCAAAGAAGTGCTTGGTGAAGTACGTACAGACCGTCCTGACGGTTTATATACCACCCTAGTTGTCGACCAATATGAGCGTTGTCTAGGGTTGGTGTATTCTTCGAAGAAATCTATAGCAAAGGCCATCGATTTGGGTCGTGGCGTTTATTATTCTCGTTCTAGGAATGAAATCTGGATCAAGGGTGAAACTTCTGGCAATGGCCAAAAGCTTTTACAAATCTCTACTGACTGTGATTCGGATGCCTTAAAGTTTATCGTTGAACAAGAAAACGTTGGATTTTGCCACTTGGAGACCATGTCTTGCTTTGGTGAATTCAAGCATGGTTTGGTGGGGCTAGAATCTTTACTAAAACAAAGGCTACAGGACGCTCCAGAGGAATCTTATACTAGAAGACTATTCAACGACTCTGCATTGTTAGATGCCAAGATCAAGGAAGAAGCTGAAGAACTGACTGAGGCAAAGGGTAAGAAGGAGCTTTCTTGGGAGGCTGCCGATTTGTTCTACTTTGCACTGGCCAAATTAGTGGCCAACGATGTTTCATTGAAGGACGTCGAGAATAATCTGAATATGAAGCATCTGAAGGTTACAAGACGGAAAGGTGATGCTAAGCCAAAGTTTGTTGGACAACCAAAGGCTGAAGAAGAAAAACTGACCGGTCCAATTCACTTGGACGTGGTGAAGGCTTCCGACAAAGTTGGTGTGCAGAAGGCTTTGAGCAGACCAATCCAAAAGACTTCTGAAATTATGTATTTAGTCAATCCGATCATCGAAAATGTTAGAGACAAAGGTAACTCTGTTTTTTTGGAGTACACAGAAAAGTTTGATGGTGTAAAATTATCCAATCCTGTTCTTAATGCTCCATTCCCAGAAGAATACTTTGAAGGTTTAACCGAGGAAATGAAGGAAGCTTTGAACCTTTCAATTGAAAACGTCCGCAAATTCCATGCTGCTCAATTGCCAACAGAGACTCTTGAAGTTGAAACCCAACCTGGTGTCTTGTGTTCCAGATTCCCTCGTCCTATTGAAAAAGTTGGTTTGTATATCCCTGGTGGCACTGCCATTTTACCAAGTACTGCATTAATGCTTGGTGTTCCAGCACAAGTTGCCCAATGTAAGGAGATTGTGTTTGCATCTCCACCAAGAAAATCTGATGGTAAAGTTTCACCCGAAGTTGTTTATGTCGCAGAAAAAGTTGGCGCTTCCAAGATTGTTCTAGCTGGTGGTGCCCAAGCCGTTGCTGCTATGGCTTACGGGACAGAAACTATTCCTAAAGTGGATAAGATCTTGGGTCCAGGTAATCAATTTGTGACTGCCGCCAAAATGTATGTTCAAAATGACACTCAAGCTCTATGTTCCATTGATATGCCAGCTGGCCCAAGTGAAGTTTTGGTTATTGCCGATGAAGATGCCGATGTGGATTTTGTTGCAAGTGATTTGCTATCGCAAGCTGAACACGGTATTGACTCCCAAGTTATCCTTGTTGGTGTTAACTTGAGCGAAAAGAAAATTCAAGAGATTCAAGATGCTGTTCACAATCAAGCTTTACAACTGCCACGTGTGGATATTGTTCGTAAATGTATTGCTCACAGTACGATCGTTCTTTGTGACGGTTACGAAGAAGCCCTTGAAATGTCCAACCAATATGCACCAGAACATTTGATTCTACAAATCGCCAATGCTAACGATTATGTTAAATTGGTTGACAATGCAGGGTCCGTATTTGTGGGTGCTTACACTCCAGAATCGTGCGGTGACTATTCAAGTGGTACTAACCATACATTACCAACCTATGGTTACGCTAGGCAGTACAGTGGTGCCAACACTGCAACCTTCCAAAAGTTTATCACTGCCCAAAACATTACCCCTGAAGGTTTAGAAAACATCGGTAGAGCTGTTATGTGCGTTGCCAAGAAGGAGGGTCTAGACGGTCACAGAAACGCTGTGAAAATCAGAATGAGTAAGCTTGGGTTGTTCCCAAAGGATTTCCAGTAG","protein_sequence":"MVLPILPLIDDLASWNSKKEYVSLVGQVLLDGSSLSNEEILQFSKEEEVPLVALSLPSGKFSDDEIIAFLNNGVSSLFIASQDAKTAEHLVEQLNVPKERVVVEENGVFSNQFMVKQKFSQDKIVSIKKLSKDMLTKEVLGEVRTDRPDGLYTTLVVDQYERCLGLVYSSKKSIAKAIDLGRGVYYSRSRNEIWIKGETSGNGQKLLQISTDCDSDALKFIVEQENVGFCHLETMSCFGEFKHGLVGLESLLKQRLQDAPEESYTRRLFNDSALLDAKIKEEAEELTEAKGKKELSWEAADLFYFALAKLVANDVSLKDVENNLNMKHLKVTRRKGDAKPKFVGQPKAEEEKLTGPIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKLGLIPKDFQ"}]}