{"ymdb_id":"YMDB00183","created_at":"2011-05-29T16:04:41.000Z","updated_at":"2016-09-08T18:35:09.000Z","name":"3-Dehydrosphinganine","cas":"16105-69-4","state":"Solid","melting_point":"","description":"3-Dehydrosphinganine is an intermediate in sphingolipid metabolism pathway. Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannosyl-diinositol-phosphorylceramide (M(IP)2C). Sphingolipid long chain bases (LCBs) - dihydrosphingosine (DHS) and phytosphingosine (PHS) - are implicated as secondary messengers in vital signaling pathways. [Biocyc SPHINGOLIPID-SYN-PWY]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"endoplasmic reticulum","synthesis_reference":null,"chebi_id":"17862","hmdb_id":"HMDB01480","kegg_id":"C02934","pubchem_id":"631","cs_id":"388895","foodb_id":null,"wikipedia_link":null,"biocyc_id":"DEHYDROSPHINGANINE","iupac":"(2S)-2-amino-1-hydroxyoctadecan-3-one","traditional_iupac":"3-ketosphinganine","logp":"5.183932733333332","pka":"15.776671018108974","alogps_solubility":"1.29e-03 g/l","alogps_logp":"5.45","alogps_logs":"-5.36","acceptor_count":"3","donor_count":"2","rotatable_bond_count":"16","polar_surface_area":"63.32000000000001","refractivity":"90.032","polarizability":"39.55737245748067","formal_charge":"0","physiological_charge":"1","pka_strongest_basic":"7.5357847026034985","pka_strongest_acidic":"14.375515999596963","bioavailability":"0","number_of_rings":"0","rule_of_five":"0","ghose_filter":"1","veber_rule":"0","mddr_like_rule":"0","synonyms":["(2S)-2-amino-1-hydroxyoctadecan-3-one","1-Hydroxy-2-amino-3-oxo-octadecane","2-amino-1-hydroxy-3-Octadecanone","3-Dehydro-D-sphinganine","3-dehydrosphinganine","3-ketodihydrosphingosine","3-Ketosphinganine","KDHS","Ketodihydrosphingosine"],"pathways":[{"name":"Sphingolipid metabolism","kegg_map_id":"00600"},{"name":"Biosynthesis of unsaturated fatty acids","kegg_map_id":"01040"},{"name":"Biosynthesis of unsaturated fatty acids (docosanoyl)","kegg_map_id":null},{"name":"Biosynthesis of unsaturated fatty acids (icosanoyl)","kegg_map_id":null},{"name":"Biosynthesis of unsaturated fatty acids (stearoyl)","kegg_map_id":null},{"name":"Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)","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":12531550,"citation":"Obeid, L. M., Okamoto, Y., Mao, C. (2002). \"Yeast sphingolipids: metabolism and biology.\" Biochim Biophys Acta 1585:163-171."}],"proteins":[{"created_at":"2011-05-24T21:32:47.000Z","updated_at":"2011-05-27T15:00:58.000Z","name":"Serine palmitoyltransferase 1","uniprot_id":"P25045","uniprot_name":"LCB1_YEAST","enzyme":true,"transporter":false,"gene_name":"LCB1","num_residues":558,"molecular_weight":"62206.60156","theoretical_pi":"6.1","general_function":"Involved in transferase activity, transferring nitrogenous groups","specific_function":"Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine","reactions":[{"id":1962,"direction":"\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2391,"direction":"\u003e","locations":"Cytoplasm. Endoplasmic reticulum. Membrane; Multi-pass membrane protein (Potential);Cytoplasm. Endoplasmic reticulum membrane; Multi-pass membrane protein","altext":"Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2).","export":false,"pw_reaction_id":null,"source":null},{"id":3861,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006382","source":"Smpdb"},{"id":3891,"direction":null,"locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006410","source":"Smpdb"},{"id":3892,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006826","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"50-84;342-371;425-457","pdb_id":null,"cellular_location":"Cytoplasm. Endoplasmic reticulum membrane; Multi-pass membrane protein","genbank_gene_id":"AY693052","genbank_protein_id":"51013555","gene_card_id":"LCB1","chromosome_location":"chromosome 13","locus":"YMR296C","synonyms":["SPT 1","SPT1","Long chain base biosynthesis protein 1"],"enzyme_classes":["2.3.1.50"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" transferase activity, transferring nitrogenous groups"},{"category":"Function","description":" cofactor binding"},{"category":"Function","description":" pyridoxal phosphate binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Aminotran_1_2","identifier":"PF00155"}],"pathways":[{"name":"Sphingolipid metabolism","kegg_map_id":"00600"},{"name":"Biosynthesis of unsaturated fatty acids","kegg_map_id":"01040"},{"name":"Biosynthesis of unsaturated fatty acids (icosanoyl)","kegg_map_id":null},{"name":"Biosynthesis of unsaturated fatty acids (stearoyl)","kegg_map_id":null}],"gene_sequence":"ATGGCACACATCCCAGAGGTTTTACCCAAATCAATACCGATTCCGGCATTTATTGTTACCACCTCATCGTACCTATGGTACTACTTCAATCTGGTGTTGACTCAAATCCCGGGAGGCCAATTCATCGTTTCGTACATCAAGAAATCGCATCATGACGATCCATACAGGACCACGGTTGAGATAGGGCTTATTTTATACGGGATCATCTATTACTTGTCCAAGCCACAACAGAAAAAGAGTCTTCAAGCACAGAAGCCCAACCTATCGCCCCAGGAGATTGACGCGCTAATTGAGGACTGGGAGCCCGAGCCTCTAGTCGACCCTTCTGCCACCGATGAGCAATCGTGGAGGGTGGCCAAAACACCCGTCACCATGGAAATGCCCATTCAGAACCATATTACTATCACCAGAAACAACCTGCAGGAGAAGTATACCAATGTTTTCAATTTGGCCTCGAACAACTTTTTGCAATTGTCCGCTACGGAGCCCGTGAAAGAAGTGGTCAAGACCACTATCAAGAATTACGGTGTGGGCGCCTGTGGTCCCGCCGGGTTCTACGGTAACCAGGACGTTCATTACACGTTGGAATATGATTTAGCACAGTTCTTTGGCACCCAAGGTTCCGTTCTGTACGGGCAAGACTTTTGTGCCGCACCCTCTGTTCTGCCTGCTTTCACAAAGCGTGGTGATGTTATCGTGGCAGACGACCAGGTGTCATTACCAGTGCAAAATGCTCTGCAACTAAGCAGATCCACAGTCTACTACTTCAACCACAACGATATGAATTCGCTAGAATGTTTATTAAACGAGTTGACCGAACAGGAGAAACTTGAGAAACTGCCCGCCATTCCAAGAAAATTTATCGTCACTGAGGGTATTTTCCACAACTCGGGCGATTTAGCTCCGTTGCCTGAGTTGACTAAGCTGAAGAACAAGTACAAGTTCAGACTATTTGTTGACGAAACCTTCTCCATTGGTGTTCTTGGCGCTACGGGCCGTGGGTTGTCAGAGCACTTCAACATGGATCGCGCAACTGCCATTGACATTACCGTTGGGTCCATGGCCACCGCGTTGGGGTCCACCGGTGGTTTTGTCCTGGGTGACAGTGTTATGTGTTTGCACCAGCGTATTGGTTCCAATGCATATTGTTTTTCTGCCTGTTTGCCGGCTTACACCGTCACATCCGTCTCCAAAGTCTTGAAATTGATGGACTCCAACAACGACGCCGTCCAGACGCTGCAAAAACTATCCAAATCTTTGCATGATTCCTTTGCATCTGACGACTCCTTGCGTTCATACGTAATCGTCACGTCCTCTCCAGTGTCTGCTGTCCTACATCTGCAACTGACTCCCGCATATAGGTCTCGCAAGTTCGGATACACCTGCGAACAGCTATTCGAAACCATGTCAGCTTTGCAAAAGAAGTCCCAGACAAACAAATTCATTGAGCCATACGAAGAGGAGGAAAAATTTCTGCAGTCCATAGTAGATCATGCTCTTATTAACTACAACGTTCTCATCACAAGAAACACTATTGTTTTAAAACAGGAGACGCTACCAATTGTCCCTAGCTTGAAAATCTGCTGTAACGCCGCCATGTCCCCAGAGGAACTCAAAAATGCTTGCGAAAGTGTCAAGCAGTCCATCCTTGCCTGTTGCCAAGAATCTAATAAATAA","protein_sequence":"MAHIPEVLPKSIPIPAFIVTTSSYLWYYFNLVLTQIPGGQFIVSYIKKSHHDDPYRTTVEIGLILYGIIYYLSKPQQKKSLQAQKPNLSPQEIDALIEDWEPEPLVDPSATDEQSWRVAKTPVTMEMPIQNHITITRNNLQEKYTNVFNLASNNFLQLSATEPVKEVVKTTIKNYGVGACGPAGFYGNQDVHYTLEYDLAQFFGTQGSVLYGQDFCAAPSVLPAFTKRGDVIVADDQVSLPVQNALQLSRSTVYYFNHNDMNSLECLLNELTEQEKLEKLPAIPRKFIVTEGIFHNSGDLAPLPELTKLKNKYKFRLFVDETFSIGVLGATGRGLSEHFNMDRATAIDITVGSMATALGSTGGFVLGDSVMCLHQRIGSNAYCFSACLPAYTVTSVSKVLKLMDSNNDAVQTLQKLSKSLHDSFASDDSLRSYVIVTSSPVSAVLHLQLTPAYRSRKFGYTCEQLFETMSALQKKSQTNKFIEPYEEEEKFLQSIVDHALINYNVLITRNTIVLKQETLPIVPSLKICCNAAMSPEELKNACESVKQSILACCQESNK"},{"created_at":"2011-05-26T16:06:52.000Z","updated_at":"2011-05-27T15:00:59.000Z","name":"Serine palmitoyltransferase 2","uniprot_id":"P40970","uniprot_name":"LCB2_YEAST","enzyme":true,"transporter":false,"gene_name":"LCB2","num_residues":561,"molecular_weight":"63110.19922","theoretical_pi":"8.19","general_function":"Involved in transferase activity","specific_function":"Catalytic subunit of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine","reactions":[{"id":1962,"direction":"\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2391,"direction":"\u003e","locations":"Cytoplasm. Endoplasmic reticulum. Membrane; Multi-pass membrane protein (Potential);Cytoplasm. Endoplasmic reticulum membrane; Multi-pass membrane protein","altext":"Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"57-77;443-463","pdb_id":null,"cellular_location":"Cytoplasm. Endoplasmic reticulum. Membrane; Multi-pass membrane protein (Potential)","genbank_gene_id":"AY723771","genbank_protein_id":"51830228","gene_card_id":"LCB2","chromosome_location":"chromosome 4","locus":"YDR062W","synonyms":["SPT 2","Long chain base biosynthesis protein 2"],"enzyme_classes":["2.3.1.50"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" transferase activity, transferring nitrogenous groups"},{"category":"Function","description":" cofactor binding"},{"category":"Function","description":" pyridoxal phosphate binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Aminotran_1_2","identifier":"PF00155"}],"pathways":[{"name":"Sphingolipid metabolism","kegg_map_id":"00600"}],"gene_sequence":"ATGAGTACTCCTGCAAACTATACCCGTGTGCCCCTGTGCGAACCAGAGGAGCTGCCAGACGACATACAAAAAGAAAATGAATATGGTACACTAGATTCTCCGGGGCATTTGTATCAAGTCAAGTCACGTCATGGGAAGCCACTACCTGAGCCCGTTGTCGACACCCCTCCTTATTACATTTCTTTGTTAACATATCTAAATTATTTGATTCTGATTATATTAGGTCATGTTCACGACTTCTTAGGTATGACCTTCCAAAAAAACAAACATCTGGATCTTTTAGAGCATGATGGGTTAGCACCTTGGTTTTCAAATTTCGAGAGTTTTTATGTCAGGAGAATTAAAATGAGAATTGATGATTGCTTTTCTAGACCAACTACTGGTGTTCCTGGTAGATTTATTCGTTGTATTGATAGAATTTCTCATAATATAAATGAGTATTTTACCTACTCAGGCGCAGTGTATCCATGCATGAACTTATCATCATATAACTATTTAGGCTTCGCACAAAGTAAGGGTCAATGTACCGATGCCGCCTTGGAATCTGTCGATAAATATTCTATTCAATCTGGTGGTCCAAGAGCTCAAATCGGTACCACAGATTTGCACATTAAAGCAGAGAAATTAGTTGCTAGATTTATCGGTAAGGAGGATGCCCTCGTTTTTTCGATGGGTTATGGTACAAATGCAAACTTGTTCAACGCTTCCCTCGATAAAAAGTGTTTAGTTATCTCTGACGAATTGAACCACACCTCTATTAGAACAGGTGTTAGGCTTTCTGGTGCTGCTGTGCGAACTTTCAAGCATGGTGATATGGTGGGTTTAGAAAAGCTTATCAGAGAACAGATAGTACTTGGTCAACCAAAAACAAATCGTCCATGGAAGAAAATTTTAATTTGCGCAGAAGGGTTGTTTTCCATGGAAGGTACTTTGTGTAACTTGCCAAAATTGGTTGAATTGAAGAAGAAATATAAATGTTACTTGTTTATCGATGAAGCCCATTCTATAGGCGCTATGGGCCCAACTGGTCGCGGTGTTTGTGAAATATTTGGCGTTGATCCCAAGGACGTCGACATTCTAATGGGTACTTTCACTAAGTCGTTTGGTGCTGCTGGTGGTTACATTGCTGCTGATCAATGGATTATCGATAGACTGAGGTTGGATTTAACCACTGTGAGTTATAGTGAGTCAATGCCGGCTCCTGTTTTAGCTCAAACTATTTCCTCATTACAAACCATTAGTGGTGAAATATGTCCCGGACAAGGTACTGAAAGATTGCAACGTATAGCCTTTAATTCCCGTTATCTACGTTTAGCTTTGCAAAGGTTAGGATTTATTGTCTACGGTGTGGCTGACTCACCAGTTATTCCCTTACTACTGTATTGTCCCTCAAAGATGCCCGCATTTTCGAGAATGATGTTACAAAGACGGATTGCTGTTGTTGTTGTTGCTTATCCTGCTACTCCGCTGATCGAATCAAGAGTAAGATTCTGTATGTCTGCATCTTTAACAAAGGAAGATATCGATTATTTACTGCGTCATGTTAGTGAAGTTGGTGACAAATTGAATTTGAAATCAAATTCCGGCAAATCCAGTTACGACGGTAAACGTCAAAGATGGGACATCGAGGAAGTTATCAGGAGAACACCTGAAGATTGCAAGGACGACAAGTATTTTGTTAATTGA","protein_sequence":"MSTPANYTRVPLCEPEELPDDIQKENEYGTLDSPGHLYQVKSRHGKPLPEPVVDTPPYYISLLTYLNYLILIILGHVHDFLGMTFQKNKHLDLLEHDGLAPWFSNFESFYVRRIKMRIDDCFSRPTTGVPGRFIRCIDRISHNINEYFTYSGAVYPCMNLSSYNYLGFAQSKGQCTDAALESVDKYSIQSGGPRAQIGTTDLHIKAEKLVARFIGKEDALVFSMGYGTNANLFNAFLDKKCLVISDELNHTSIRTGVRLSGAAVRTFKHGDMVGLEKLIREQIVLGQPKTNRPWKKILICAEGLFSMEGTLCNLPKLVELKKKYKCYLFIDEAHSIGAMGPTGRGVCEIFGVDPKDVDILMGTFTKSFGAAGGYIAADQWIIDRLRLDLTTVSYSESMPAPVLAQTISSLQTISGEICPGQGTERLQRIAFNSRYLRLALQRLGFIVYGVADSPVIPLLLYCPSKMPAFSRMMLQRRIAVVVVAYPATPLIESRVRFCMSASLTKEDIDYLLRHVSEVGDKLNLKSNSGKSSYDGKRQRWDIEEVIRRTPEDCKDDKYFVN"},{"created_at":"2011-05-27T03:19:47.000Z","updated_at":"2011-07-22T17:53:45.000Z","name":"3-ketodihydrosphingosine reductase TSC10","uniprot_id":"P38342","uniprot_name":"TSC10_YEAST","enzyme":true,"transporter":false,"gene_name":"TSC10","num_residues":320,"molecular_weight":"35986.19922","theoretical_pi":"6.25","general_function":"Involved in oxidoreductase activity","specific_function":"Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS)","reactions":[{"id":1164,"direction":"\u003c\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2718,"direction":"\u003e","locations":"Endoplasmic reticulum membrane; Single-pass membrane protein (Potential)","altext":"Sphinganine + NADP(+) = 3-dehydrosphinganine + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":3890,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006409","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"280-300","pdb_id":null,"cellular_location":"Endoplasmic reticulum membrane; Single-pass membrane protein (Potential)","genbank_gene_id":"X70529","genbank_protein_id":"296564","gene_card_id":"TSC10","chromosome_location":"chromosome 2","locus":"YBR265W","synonyms":["3-dehydrosphinganine reductase","KDS reductase","Temperature-sensitive CSG2 suppressor protein 10"],"enzyme_classes":["1.1.1.102"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"adh_short","identifier":"PF00106"}],"pathways":[{"name":"Sphingolipid metabolism","kegg_map_id":"00600"},{"name":"Biosynthesis of unsaturated fatty acids","kegg_map_id":"01040"}],"gene_sequence":"ATGAAGTTTACGTTAGAAGACCAAGTTGTGTTGATCACTGGTGGTTCACAAGGTCTTGGAAAGGAATTCGCCAAAAAATATTATAATGAGGCTGAAAACACAAAGATTATTATCGTCAGTAGGTCAGAGGCTAGACTGCTGGACACATGCAACGAAATTAGGATTGAAGCTCACCTGAGAAGGGAAACCACTGACGAGGGCCAAGTGCAACATAAGTTGGCTGCGCCCTTGGACCTTGAGCAACGGTTATTTTACTACCCATGCGACTTGTCCTGCTACGAATCCGTGGAATGTTTGTTCAATGCCCTGAGAGACTTGGATTTACTCCCTACACAAACGTTATGCTGTGCAGGGGGGGCTGTTCCTAAGTTATTTCGTGGGCTAAGCGGACATGAGTTGAACTTGGGTATGGACATCAACTATAAAACAACTTTGAACGTGGCACATCAGATTGCCCTTGCAGAGCAAACCAAGGAACACCACCTCATCATCTTTTCTAGTGCCACCGCGCTTTACCCATTTGTGGGCTATTCCCAGTATGCGCCTGCAAAAGCTGCAATCAAATCACTGGTAGCAATCTTAAGACAAGAACTGACGAACTTCCGTATCAGTTGTGTTTATCCTGGTAATTTTGAAAGCGAAGGTTTCACTGTAGAGCAGCTAACGAAACCCGAAATTACAAAGTTGATCGAAGGCCCCTCAGACGCTATCCCATGCAAACAAGCATGTGATATCATTGCCAAGTCGCTGGCCAGAGGTGATGAAGACGTTTTTACAGATTTTGTCGGATGGATGATAATGGGGATGGACCTTGGGCTCACCGCAAAGAAAAGCCGCTTTGTTCCGTTGCAATGGATTTTTGGTGTCCTATCAAACATTCTGGTCGTGCCATTCTACATGGTTGGCTGTTCCTGGTATATCAGGAAATGGTTTCGTGAAAATGACGGCAAGAAGGCCAACTGA","protein_sequence":"MKFTLEDQVVLITGGSQGLGKEFAKKYYNEAENTKIIIVSRSEARLLDTCNEIRIEAHLRRETTDEGQVQHKLAAPLDLEQRLFYYPCDLSCYESVECLFNALRDLDLLPTQTLCCAGGAVPKLFRGLSGHELNLGMDINYKTTLNVAHQIALAEQTKEHHLIIFSSATALYPFVGYSQYAPAKAAIKSLVAILRQELTNFRISCVYPGNFESEGFTVEQLTKPEITKLIEGPSDAIPCKQACDIIAKSLARGDEDVFTDFVGWMIMGMDLGLTAKKSRFVPLQWIFGVLSNILVVPFYMVGCSWYIRKWFRENDGKKAN"}]}