{"ymdb_id":"YMDB00019","created_at":"2011-05-29T15:49:01.000Z","updated_at":"2016-09-08T18:34:54.000Z","name":"Saccharopine","cas":"997-68-2","state":"Solid","melting_point":"247-250 oC","description":"Saccharopine is an intermediate in the biosynthesis of lysine and glutamate in yeast. It is produced from alpha-aminoadipic acid in the alpha-aminoadipic acid pathway. It was first isolated in 1961 from Saccharomyces, hence the name, by Darling and Larsen.[Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":"Burkard, Ulrike; Walther, Ingrid; Effenberger, Franz. Amino acids. 6. Investigations on the synthesis of L-saccharopin. Liebigs Annalen der Chemie (1986), (6), 1030-43. ","chebi_id":"16927","hmdb_id":"HMDB00279","kegg_id":"C00449","pubchem_id":"160556","cs_id":"141086","foodb_id":null,"wikipedia_link":"Saccharopine","biocyc_id":"SACCHAROPINE","iupac":"(2S)-2-{[(5S)-5-amino-5-carboxypentyl]amino}pentanedioic acid","traditional_iupac":"saccharopine","logp":"-5.407435330625966","pka":"2.375174811126724","alogps_solubility":"5.25e+00 g/l","alogps_logp":"-2.77","alogps_logs":"-1.72","acceptor_count":"8","donor_count":"5","rotatable_bond_count":"11","polar_surface_area":"149.95","refractivity":"63.95300000000001","polarizability":"28.138708375547512","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"10.892138404544818","pka_strongest_acidic":"1.4444535649435268","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(S)-N-(5-amino-5-carboxypentyl)-L-Glutamic acid","Epsilon-N-(L-Glutar-2-yl)-L-lysine","L-N-(5-amino-5-carboxypentyl)-Glutamic acid","L-Saccharopin","L-Saccharopine","N-(5-amino-5-carboxypentyl)-glutamic acid","N-(5-amino-5-carboxypentyl)-L-glutamic acid","N-[(5S)-5-amino-5-carboxypentyl]-L-Glutamic acid","N-[(S)-5-amino-5-Carboxypentyl]-L-glutamate","N-[(S)-5-amino-5-Carboxypentyl]-L-glutamic acid","N(6)-(L-1,3-dicarboxypropyl)-L-lysine","N6-(L-1,3-Dicarboxypropyl)-L-lysine","Saccharopin"],"pathways":[{"name":"Lysine degradation","kegg_map_id":"00310"},{"name":"Lysine biosynthesis","kegg_map_id":"00300"},{"name":"lysine metabolism","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":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":17002315,"citation":"Xu, H., West, A. H., Cook, P. F. (2006). \"Overall kinetic mechanism of saccharopine dehydrogenase from Saccharomyces cerevisiae.\" Biochemistry 45:12156-12166."},{"pubmed_id":4287986,"citation":"Saunders, P. P., Broquist, H. P. (1966). \"Saccharopine, an intermediate of the aminoadipic acid pathway of lysine biosynthesis. IV. Saccharopine dehydrogenase.\" J Biol Chem 241:3435-3440."},{"pubmed_id":3123231,"citation":"Ramos, F., Dubois, E., Pierard, A. (1988). \"Control of enzyme synthesis in the lysine biosynthetic pathway of Saccharomyces cerevisiae. Evidence for a regulatory role of gene LYS14.\" Eur J Biochem 171:171-176."},{"pubmed_id":3928261,"citation":"Bhattacharjee, J. K. (1985). \"alpha-Aminoadipate pathway for the biosynthesis of lysine in lower eukaryotes.\" Crit Rev Microbiol 12:131-151."}],"proteins":[{"created_at":"2011-05-24T20:17:41.000Z","updated_at":"2011-05-29T14:08:01.000Z","name":"Saccharopine dehydrogenase [NAD+, L-lysine-forming]","uniprot_id":"P38998","uniprot_name":"LYS1_YEAST","enzyme":true,"transporter":false,"gene_name":"LYS1","num_residues":373,"molecular_weight":"41464.39844","theoretical_pi":"9.56","general_function":"Involved in oxidoreductase activity","specific_function":"Catalyzes the NAD(+)-dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate","reactions":[{"id":1959,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2309,"direction":"\u003e","locations":"Cytoplasm","altext":"N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NAD(+) + H(2)O = L-lysine + 2-oxoglutarate + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":4179,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006478","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"X77362","genbank_protein_id":"453184","gene_card_id":"LYS1","chromosome_location":"chromosome 9","locus":"YIR034C","synonyms":["SDH","Lysine--2-oxoglutarate reductase"],"enzyme_classes":["1.5.1.7","1.5.1.8"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"AlaDh_PNT_C","identifier":"PF01262"},{"name":"AlaDh_PNT_N","identifier":"PF05222"}],"pathways":[{"name":"Lysine biosynthesis","kegg_map_id":"00300"},{"name":"Lysine degradation","kegg_map_id":"00310"},{"name":"lysine metabolism","kegg_map_id":null}],"gene_sequence":"ATGGCTGCCGTCACATTACATCTAAGAGCTGAAACTAAACCCCTAGAGGCACGTGCTGCCTTAACACCTACCACGGTTAAAAAACTGATAGCTAAGGGCTTCAAAATATATGTAGAGGACAGTCCACAATCTACTTTCAATATTAACGAATATCGTCAAGCAGGTGCCATTATAGTGCCTGCAGGTTCATGGAAAACCGCTCCACGCGACAGAATCATTATAGGTTTGAAGGAAATGCCTGAAACCGATACTTTCCCTCTAGTCCACGAACACATCCAGTTTGCTCACTGCTACAAAGACCAAGCTGGGTGGCAAAATGTCCTTATGAGATTTATTAAGGGACACGGTACTCTATATGATTTGGAATTTTTGGAAAATGACCAAGGTAGAAGAGTTGCTGCCTTTGGATTTTACGCTGGGTTCGCAGGTGCAGCCCTTGGTGTAAGAGACTGGGCATTCAAGCAAACGCATTCTGACGATGAAGACTTGCCTGCAGTGTCGCCTTACCCCAATGAAAAGGCGTTGGTTAAAGATGTTACCAAAGATTATAAAGAAGCCTTAGCCACCGGCGCCAGAAAGCCAACCGTGTTAATCATTGGTGCGCTAGGAAGATGTGGTTCCGGTGCCATCGATCTGTTGCACAAAGTTGGTATTCCAGATGCTAACATATTAAAATGGGATATCAAAGAAACTTCCCGTGGTGGTCCCTTTGACGAAATTCCACAAGCTGATATTTTCATCAATTGTATATATCTATCGAAGCCAATTGCTCCTTTCACTAACATGGAGAAACTGAATAATCCTAACAGAAGACTAAGGACCGTGGTGGACGTATCAGCAGACACTACCAACCCTCACAACCCCATCCCAATATACACTGTGGCTACTGTGTTTAACAAACCTACCGTTCTGGTACCTACCACTGTCGGGCCTAAATTATCTGTCATCTCTATTGATCACTTGCCTTCTTTGCTGCCAAGAGAAGCTTCAGAATTTTTCTCTCATGATCTTTTACCATCTTTAGAGCTCCTACCTCAAAGAAAAACTGCTCCTGTCTGGGTTAGAGCCAAGAAATTGTTCGATAGACATTGCGCTCGTGTTAAAAGATCTTCAAGATTGTAG","protein_sequence":"MAAVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEMPETDTFPLVHEHIQFAHCYKDQAGWQNVLMRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNMEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARVKRSSRL"},{"created_at":"2011-05-24T20:18:23.000Z","updated_at":"2011-05-27T14:56:00.000Z","name":"Saccharopine dehydrogenase [NADP+, L-glutamate-forming]","uniprot_id":"P38999","uniprot_name":"LYS9_YEAST","enzyme":true,"transporter":false,"gene_name":"LYS9","num_residues":446,"molecular_weight":"48917.30078","theoretical_pi":"4.87","general_function":"Involved in binding","specific_function":"N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NADP(+) + H(2)O = L-glutamate + L-2-aminoadipate 6-semialdehyde + NADPH","reactions":[{"id":1960,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2310,"direction":"\u003e","locations":null,"altext":"N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NADP(+) + H(2)O = L-glutamate + L-2-aminoadipate 6-semialdehyde + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":4178,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006477","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X77363","genbank_protein_id":"453186","gene_card_id":"LYS9","chromosome_location":"chromosome 14","locus":"YNR050C","synonyms":["Saccharopine reductase"],"enzyme_classes":["1.5.1.10"],"go_classes":[],"pfams":[{"name":"Saccharop_dh","identifier":"PF03435"}],"pathways":[{"name":"Lysine biosynthesis","kegg_map_id":"00300"},{"name":"Lysine degradation","kegg_map_id":"00310"},{"name":"lysine metabolism","kegg_map_id":null}],"gene_sequence":"ATGGGAAAGAACGTTTTGTTGCTAGGATCTGGTTTTGTTGCACAACCTGTTATCGACACATTGGCTGCTAATGATGACATCAATGTCACTGTCGCATGTAGAACATTAGCCAATGCGCAAGCATTGGCCAAGCCCTCTGGATCCAAGGCTATTTCATTGGATGTTACCGATGACAGTGCCTTAGACAAAGTTCTGGCTGATAACGATGTTGTCATCTCTTTGATTCCATACACCTTCCATCCAAATGTGGTAAAGAGCGCCATCAGAACAAAGACCGATGTCGTCACTTCCTCTTACATCTCACCTGCCTTAAGAGAATTGGAACCAGAAATCGTAAAGGCAGGTATTACAGTTATGAACGAAATTGGGTTGGATCCAGGTATCGACCACTTGTATGCGGTCAAGACTATTGATGAAGTTCACAGAGCTGGTGGTAAGCTAAAGTCATTCTTGTCATACTGTGGTGGTTTACCAGCTCCTGAAGACTCTGATAATCCATTAGGATACAAATTTTCATGGTCCTCCAGAGGTGTGCTACTGGCTTTAAGAAACTCTGCTAAATACTGGAAAGACGGAAAGATTGAAACTGTTTCTTCCGAAGACTTAATGGCCACTGCTAAGCCTTACTTCATCTACCCAGGTTATGCATTCGTTTGCTACCCAAATAGAGACTCTACCCTTTTCAAGGATCTTTATCATATTCCAGAAGCCGAAACGGTCATTAGAGGTACTTTGAGATATCAAGGTTTCCCAGAATTTGTTAAGGCTTTAGTTGACATGGGTATGTTGAAGGATGATGCTAACGAAATCTTCAGCAAGCCAATTGCCTGGAACGAAGCACTAAAACAATATTTAGGTGCCAAGTCTACTTCTAAAGAAGATTTGATTGCTTCCATTGACTCAAAGGCTACTTGGAAAGATGATGAAGATAGAGAAAGAATCCTTTCCGGGTTTGCTTGGTTAGGCTTGTTCTCTGACGCAAAGATCACACCAAGAGGTAATGCTTTAGACACTCTATGTGCACGTTTAGAAGAACTAATGCAATATGAAGACAATGAAAGAGATATGGTTGTACTACAACACAAATTCGGTATTGAATGGGCTGATGGAACTACCGAAACAAGAACATCCACTTTAGTTGACTATGGTAAGGTTGGTGGTTACAGTTCTATGGCCGCTACTGTTGGTTATCCAGTTGCCATTGCAACGAAATTCGTCTTAGATGGTACAATCAAGGGACCAGGCTTACTAGCGCCATACTCACCAGAGATTAATGATCCAATCATGAAAGAACTAAAGGACAAGTACGGCATCTATCTAAAGGAAAAGACAGTGGCTTAA","protein_sequence":"MGKNVLLLGSGFVAQPVIDTLAANDDINVTVACRTLANAQALAKPSGSKAISLDVTDDSALDKVLADNDVVISLIPYTFHPNVVKSAIRTKTDVVTSSYISPALRELEPEIVKAGITVMNEIGLDPGIDHLYAVKTIDEVHRAGGKLKSFLSYCGGLPAPEDSDNPLGYKFSWSSRGVLLALRNSAKYWKDGKIETVSSEDLMATAKPYFIYPGYAFVCYPNRDSTLFKDLYHIPEAETVIRGTLRYQGFPEFVKALVDMGMLKDDANEIFSKPIAWNEALKQYLGAKSTSKEDLIASIDSKATWKDDEDRERILSGFAWLGLFSDAKITPRGNALDTLCARLEELMQYEDNERDMVVLQHKFGIEWADGTTETRTSTLVDYGKVGGYSSMAATVGYPVAIATKFVLDGTIKGPGLLAPYSPEINDPIMKELKDKYGIYLKEKTVA"}]}