{"ymdb_id":"YMDB00102","created_at":"2011-05-29T15:56:53.000Z","updated_at":"2016-09-08T18:35:01.000Z","name":"7,8-diaminononanoic acid","cas":"21738-21-6","state":null,"melting_point":null,"description":"7,8-Diaminononanoic acid is an intermediate in biotin biosynthesis, a water-soluble B-complex vitamin (vitamin B7). [Biocyc BIOTIN-SYNTHESIS-PWY]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"Cytoplasm;Extracellular","synthesis_reference":null,"chebi_id":"2247","hmdb_id":null,"kegg_id":"C01037","pubchem_id":"652","cs_id":"632","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"7,8-diaminononanoic acid","traditional_iupac":"7,8-diaminopelargonic acid","logp":"-1.9209886615753784","pka":null,"alogps_solubility":"4.94e+00 g/l","alogps_logp":"-2.11","alogps_logs":"-1.58","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"7","polar_surface_area":"89.34","refractivity":"51.29959999999999","polarizability":"21.871489528943158","formal_charge":"0","physiological_charge":"1","pka_strongest_basic":"9.969554860988813","pka_strongest_acidic":"4.728429829552393","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["7,8-DAP","7,8-DAPA","7,8-Diaminononanoate","7,8-diaminopelargonic acid","DAP","DAPA"],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"}],"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":"2011-05-26T17:20:03.000Z","updated_at":"2011-07-22T17:54:36.000Z","name":"Dethiobiotin synthetase","uniprot_id":"P53630","uniprot_name":"BIOD_YEAST","enzyme":true,"transporter":false,"gene_name":"BIO4","num_residues":237,"molecular_weight":"26256.69922","theoretical_pi":"4.79","general_function":"Involved in magnesium ion binding","specific_function":"ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin","reactions":[{"id":1449,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2473,"direction":"\u003e","locations":null,"altext":"ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin.","export":false,"pw_reaction_id":null,"source":null},{"id":3755,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006279","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY558424","genbank_protein_id":"45270738","gene_card_id":"BIO4","chromosome_location":"chromosome 14","locus":"YNR057C","synonyms":["DTB synthetase","Dethiobiotin synthase","DTBS"],"enzyme_classes":["6.3.3.3"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" magnesium ion binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" cyclo-ligase activity"},{"category":"Function","description":" ligase activity"},{"category":"Function","description":" ligase activity, forming carbon-nitrogen bonds"},{"category":"Function","description":" binding"},{"category":"Function","description":" dethiobiotin synthase activity"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"},{"category":"Process","description":" biotin metabolic process"},{"category":"Process","description":" biotin biosynthetic process"}],"pfams":[],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"name":"Biotin Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGAACAGCAAATCTCAACAACAAGAACAACAACCAATTGTATTCGTCACCGGTACAGACACTGATGTTGGTAAAACCTTTGTATCAACATTATTGGTACACAAATGGAAAGCTGCATACTGGAAACCCGTACAAACTGGAATTGAGTCAGATCAAGGTGACTCCGAGACATTGAAAAATTTCAAAATAGCCGCATCAACTTGGCAACCACCTATATTCACGCCCACTTATGCGCTGCAGAAGCCTCTATCTCCGCTCCAGGCCATGGAGTACGAACCTAATGTCGACATCAGGTTGTTGGATTTCGTAGTTCCTGAAGAGTGGAGCGCAGAGAATCCATTGGTCGTAGAAGGAGCCGGCGGGGTTTGCGTTCCTATCACTCGTAAATTGGAAATTACGACGGATCTAATTAAACATCTGATTGAGACTAGCGGCCATCCAGTGTACGTAGTTGTCGTGGCACGCAGCGGGCTAGGGACTCTGAATCATACATTGCTGACTTGGAATCATCTTTGCGATAATGGCTTGAGAAGCCACCTTTTTGGGGTCATTCTCAATGGGGAACCGAATGAAGGCAACGTGCAGGCCCTGAAGAAGTTCGGTGTCAATATTATGGCACAGGTTGCACAATGTACTACGGCACATGATCAGGATATGGAGTTGCATGAACTGCCATCGGTGGAGTCATTAATGACCCAACAAGACGTAGAATAG","protein_sequence":"MNSKSQQQEQQPIVFVTGTDTDVGKTFVSTLLVHKWKAAYWKPVQTGIESDQGDSETLKNFKIAASTWQPPIFTPTYALQKPLSPLQAMEYEPNVDIRLLDFVVPEEWSAENPLVVEGAGGVCVPITRKLEITTDLIKHLIETSGHPVYVVVVARSGLGTLNHTLLTWNHLCDNGLRSHLFGVILNGEPNEGNVQALKKFGVNIMAQVAQCTTAHDQDMELHELPSVESLMTQQDVE"},{"created_at":"2011-05-26T19:26:29.000Z","updated_at":"2011-07-22T17:54:00.000Z","name":"Adenosylmethionine-8-amino-7-oxononanoate aminotransferase","uniprot_id":"P50277","uniprot_name":"BIOA_YEAST","enzyme":true,"transporter":false,"gene_name":"BIO3","num_residues":480,"molecular_weight":"53708.39844","theoretical_pi":"6.41","general_function":"Involved in transaminase activity","specific_function":"Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor","reactions":[{"id":1274,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2566,"direction":"\u003e","locations":null,"altext":"S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate.","export":false,"pw_reaction_id":null,"source":null},{"id":3754,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006278","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AB200248","genbank_protein_id":"67772574","gene_card_id":"BIO3","chromosome_location":"chromosome 14","locus":"YNR058W","synonyms":["7,8-diamino-pelargonic acid aminotransferase","DAPA AT","DAPA aminotransferase","Diaminopelargonic acid synthase"],"enzyme_classes":["2.6.1.62"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" cofactor binding"},{"category":"Function","description":" pyridoxal phosphate binding"},{"category":"Function","description":" adenosylmethionine-8-amino-7-oxononanoate transaminase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" transferase activity, transferring nitrogenous groups"},{"category":"Function","description":" transaminase activity"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"},{"category":"Process","description":" biotin metabolic process"},{"category":"Process","description":" biotin biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"}],"pfams":[{"name":"Aminotran_3","identifier":"PF00202"}],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"name":"Biotin Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGTCCCAAGAAATTTCATATACACCAGATGTCGCGGAACTGCTAGACTTTGATAAAAAACATATTTGGCATCCTTATACGTCATTGAGTTCACCATTGAACGTTTATCCGGTAAAGAGTGCTCACGGATGCAAGCTGGTGTTGGATACCGACTCACCAGTGGACGTCGAGGTGATCGACGCCATGTCGTCGTGGTGGTGTGTTATTCACGGGTACAATAATCCAGAATTAAATGAGGCCCTTACCAAGCAGATGTTAAAGTTTTCTCACGTCCTTCTTGGTGGATTCACCCATAAAGGAGCTGTGAATCTAGTCCAAAAACTTTTAAAAGTGATTGATGAACCCTCTTTGCAGTACTGTTTCCTCGCAGATTCTGGCTCAGTAGCAGTGGAAGTAGCTTTGAAGATGGCTTTACAATCAAACATGTCAGGGGAAGCTACTAAAAATAGAACAAAATTTTTGACAATCAAGAACGGGTATCATGGTGATACATTTGGCGCTATGAGTGTTTGTGATCCTGAGAATTCTATGCATCATATCTACAACGATCGACTCAGTGAGAACATCTTCGCCCAAGCTCCCTCTATTGTCGATGGTCTTCCAACCAGCCAGAACGGTTTCGAGGACCATTGGAATGCAGAAGAAGTTACCGATCTCAAGAAGCAATTTGAATTGCATAGTGATGAGATCTGTGCTGTGATTTTGGAGCCTATCTTACAGGGTGCAGGAGGTTTGCGACCATACCATCCACAGTTCCTAATTGAAGTTCAGAAACTATGTAACCAATACGACGTTTTATTCATCATGGACGAGATTGCTACGGGATTTGGTAGAACAGGTGAGATTTTCGCATTCAAGCACTGTCAAAAATACCAGGACCAACGTGGCATCAGTCCTTCCGATCAGATCAAAGTTGTTCCTGACATATTGTGCGTTGGGAAGGGCTTAACCAGTGGATATATGACTATGAGTGCAGTGGTAGTCAACGACAAAGTTGCTTCCAGAATCTCTTCTCCAAATAGCCCTACTGGTGGCTGCTTCATGCATGGCCCCACCTTCATGGGCAATGCCCTGGCATGCAGTGTGGCAGAAAAGTCTATGGATATACTACTGCGTGGCGAGTGGAGAAAACAAGTGTCTGCAATTGAAGACCAAATTTATAGAGAACTATACCAGTACATCAAGAACCCAGATAATGGGCTCATTGGAACTGTTGTTAAGCGTGTGTCAGTTATTGGAGCTGTAGGTATCGTAGAGCTATACAAGAAGACAGATCCCGAGTGGTTCCAGAAAAAGTTTATATCCAAGGGAGTACATATCCGACCTTTCAACTGCCTGTGTTACATTATGCCACCATATGTGATCACGACAGAGGAATTGACGAAGGTTAATCAAGTCTTGATTGAAGTATTACATGAGTGGAAATCCCACATAAACCAATGA","protein_sequence":"MSQEISYTPDVAELLDFDKKHIWHPYTSLSSPLNVYPVKSAHGCKLVLDTDSPVDVEVIDAMSSWWCVIHGYNNPELNEALTKQMLKFSHVLLGGFTHKGAVNLVQKLLKVIDEPSLQYCFLADSGSVAVEVALKMALQSNMSGEATKNRTKFLTIKNGYHGDTFGAMSVCDPENSMHHIYNDRLSENIFAQAPSIVDGLPTSQNGFEDHWNAEEVTDLKKQFELHSDKICAVILEPILQGAGGLRPYHPQFLIEVQKLCNQYDVLFIMDEIATGFGRTGEIFAFKHCQKYQDQHGISPSDQIKVVPDILCVGKGLTSGYMTMSAVVVNDKVASRISSPNSPTGGCFMHGPTFMGNALACSVAEKSMDILLRGEWRKQVSAIENQIYRELYQYIKNPDNGLIGTVVKRVSVIGAVGIVELYKKTDPEWFQKKFISKGVHIRPFNCLCYIMPPYVITTEELTKVNQVLIEVLHEWKSHINQ"}]}