{"ymdb_id":"YMDB16140","created_at":"2016-09-12T18:14:41.000Z","updated_at":"2016-10-17T22:34:41.000Z","name":"Diaminopimelic acid","cas":null,"state":"Solid","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":"(2S,6S)-2,6-diaminoheptanedioic acid","traditional_iupac":"diamino-pimelic acid","logp":"-5.545367993935247","pka":"2.585040505515717","alogps_solubility":"1.41e+01 g/l","alogps_logp":"-4.13","alogps_logs":"-1.13","acceptor_count":"6","donor_count":"4","rotatable_bond_count":"6","polar_surface_area":"126.64000000000001","refractivity":"43.63940000000001","polarizability":"18.933170312561906","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"9.827564769536531","pka_strongest_acidic":"1.8470749826619342","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":[],"pathways":[{"name":"Biotin Biosynthesis","kegg_map_id":null}],"growth_conditions":[],"references":[],"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":" 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":"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":"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":" 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":"Function","description":" cofactor binding"},{"category":"Function","description":" pyridoxal phosphate binding"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule 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":[{"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"}]}