{"ymdb_id":"YMDB00697","created_at":"2011-05-29T18:44:21.000Z","updated_at":"2016-09-08T18:35:47.000Z","name":"lipoamide","cas":"940-69-2","state":"Solid","melting_point":"126.0-129.0 oC","description":"Lipoamide (6,8-dithiooctanoic amide) can be used to refer to protein bound lipoic acid, but this can be misleading as this is technically incorrect. Lipoyl-protein or lipoyl-domain are better terms to refer to protein bound lipoic acid. Lipoamide corresponds to the 6,8-dithiooctanoic acid attached to protein by an amide linkage. There are no reported occurrences of free lipoamide in nature.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"mitochondrion","synthesis_reference":"Xu, Yaming; Li, Zhitian; Gu, Yunlong. Synthesis of thioctamide. Faming Zhuanli Shenqing Gongkai Shuomingshu (1997), 5 pp. ","chebi_id":"17460","hmdb_id":"HMDB00962","kegg_id":"C00248","pubchem_id":"863","cs_id":"840","foodb_id":null,"wikipedia_link":"Lipoamide","biocyc_id":"LIPOAMIDE","iupac":"5-(1,2-dithiolan-3-yl)pentanamide","traditional_iupac":"lipoamide","logp":"1.3068367939999996","pka":null,"alogps_solubility":"1.01e-01 g/l","alogps_logp":"2.30","alogps_logs":"-3.31","acceptor_count":"1","donor_count":"1","rotatable_bond_count":"5","polar_surface_area":"43.09","refractivity":"56.1936","polarizability":"22.384415060709664","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-1.3815647676501084","pka_strongest_acidic":"16.449049724883853","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"1","veber_rule":"0","mddr_like_rule":"0","synonyms":["1,2-Dithiolane-3-pentanamide","1,2-Dithiolane-3-valeramide","5-(1,2-dithiolan-3-yl)-pentanamide","5-(1,2-dithiolan-3-yl)pentanamide","5-(1,2-Dithiolan-3-yl)valeramide","5-(Dithiolan-3-yl)valeramide","Alpha-lipoate","Alpha-lipoic acid","Alpha-lipoic acid amide","dl-6-Thioctic amide","DL-lipoamide","Lipamide","Lipoacin","Lipoamid","Lipoamide","Lipoicin","Lipozyme","Lypoaran","Pathoclon","Thioami","Thioctamid","Thioctamide","thioctic acid amide","Thioctic acid amide (JAN)","Thiotomin","Ticolin","Vitamin n"],"pathways":[{"name":"Citric Acid Cycle","kegg_map_id":null},{"name":"Citric Acid Cycle 1434561204","kegg_map_id":null},{"name":"TCA Cycle","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":10224250,"citation":"Przybyla-Zawislak, B., Gadde, D. M., Ducharme, K., McCammon, M. T. (1999). \"Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes.\" Genetics 152:153-166."}],"proteins":[{"created_at":"2011-05-24T20:14:31.000Z","updated_at":"2011-05-27T14:56:00.000Z","name":"Dihydrolipoyl dehydrogenase, mitochondrial","uniprot_id":"P09624","uniprot_name":"DLDH_YEAST","enzyme":true,"transporter":false,"gene_name":"LPD1","num_residues":499,"molecular_weight":"54009.69922","theoretical_pi":"8.22","general_function":"Involved in oxidoreductase activity","specific_function":"Lipoamide dehydrogenase is a component of the alpha- ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine","reactions":[{"id":2306,"direction":"\u003e","locations":"Mitochondrion matrix","altext":"Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1V59","cellular_location":"Mitochondrion matrix","genbank_gene_id":"D50617","genbank_protein_id":"836736","gene_card_id":"LPD1","chromosome_location":"chromosome 6","locus":"YFL018C","synonyms":["Dihydrolipoamide dehydrogenase","Glycine decarboxylase complex subunit L","Lipoamide dehydrogenase component of pyruvate dehydrogenase complex","Pyruvate dehydrogenase complex E3 component"],"enzyme_classes":["1.8.1.4"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" FAD or FADH2 binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" oxidoreductase activity, acting on NADH or NADPH"},{"category":"Function","description":" oxidoreductase activity, acting on a sulfur group of donors, NAD or NADP as acceptor"},{"category":"Function","description":" dihydrolipoyl dehydrogenase activity"},{"category":"Process","description":" cellular homeostasis"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cell redox homeostasis"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" cellular process"}],"pfams":[{"name":"Pyr_redox","identifier":"PF00070"},{"name":"Pyr_redox_2","identifier":"PF07992"},{"name":"Pyr_redox_dim","identifier":"PF02852"}],"pathways":[{"name":"Glycolysis / Gluconeogenesis","kegg_map_id":"00010"},{"name":"Citrate cycle (TCA cycle)","kegg_map_id":"00020"},{"name":"Glycine, serine and threonine metabolism","kegg_map_id":"00260"},{"name":"Valine, leucine and isoleucine degradation","kegg_map_id":"00280"},{"name":"Pyruvate metabolism","kegg_map_id":"00620"}],"gene_sequence":"ATGTTAAGAATCAGATCACTCCTAAATAATAAGCGTGCCTTTTCGTCCACAGTCAGGACATTGACCATTAACAAGTCACATGATGTAGTCATCATCGGTGGTGGCCCTGCTGGTTACGTGGCTGCTATCAAAGCTGCTCAATTGGGATTTAACACTGCATGTGTAGAAAAAAGAGGCAAATTAGGCGGTACCTGTCTTAACGTTGGATGTATCCCCTCCAAAGCACTTCTAAATAATTCTCATTTATTCCACCAAATGCATACGGAAGCGCAAAAGAGAGGTATTGACGTCAACGGTGATATCAAAATTAACGTAGCAAACTTCCAAAAGGCTAAGGATGACGCTGTTAAGCAATTAACTGGAGGTATTGAGCTTCTGTTCAAGAAAAATAAGGTCACCTATTATAAAGGTAATGGTTCATTCGAAGACGAAACGAAGATCAGAGTAACTCCCGTTGATGGGTTGGAAGGCACTGTCAAGGAAGACCACATACTAGATGTTAAGAACATCATAGTCGCCACGGGCTCTGAAGTTACACCCTTCCCCGGTATTGAAATAGATGAGGAAAAAATTGTCTCTTCAACAGGTGCTCTTTCGTTAAAGGAAATTCCCAAAAGATTAACCATCATTGGTGGAGGAATCATCGGATTGGAAATGGGTTCAGTTTACTCTAGATTAGGCTCCAAGGTTACTGTAGTAGAATTTCAACCTCAAATTGGTGCATCTATGGACGGCGAGGTTGCCAAAGCCACCCAAAAGTTCTTGAAAAAGCAAGGTTTGGACTTCAAATTAAGCACCAAAGTTATTTCTGCAAAGAGAAACGACGACAAGAACGTCGTCGAAATTGTTGTAGAAGATACTAAAACGAATAAGCAAGAAAATTTGGAAGCTGAAGTTTTGCTGGTTGCTGTTGGTAGAAGACCTTACATTGCTGGCTTAGGGGCTGAAAAGATTGGATTAGAAGTAGACAAAAGGGGACGCCTAGTCATTGATGACCAATTTAATTCCAAGTTCCCACACATTAAAGTGGTAGGAGATGTTACATTTGGTCCAATGCTGGCTCACAAAGCCGAAGAGGAAGGTATTGCAGCTGTCGAAATGTTGAAAACTGGTCACGGTCATGTCAACTATAACAACATTCCTTCGGTCATGTATTCTCACCCAGAAGTAGCATGGGTTGGTAAAACCGAAGAGCAATTGAAAGAAGCCGGCATTGACTATAAAATTGGTAAGTTCCCCTTTGCGGCCAATTCAAGAGCCAAGACCAACCAAGACACTGAAGGTTTCGTGAAGATTTTGATCGATTCCAAGACCGAGCGTATTTTGGGGGCTCACATTATCGGTCCAAATGCCGGTGAAATGATTGCTGAAGCTGGCTTAGCCTTAGAATATGGCGCTTCCGCAGAAGATGTTGCTAGGGTCTGCCATGCTCATCCTACTTTGTCCGAAGCATTTAAGGAAGCTAACATGGCTGCCTATGATAAAGCTATTCATTGTTGA","protein_sequence":"MLRIRSLLNNKRAFSSTVRTLTINKSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCIPSKALLNNSHLFHQMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTGGIELLFKKNKVTYYKGNGSFEDETKIRVTPVDGLEGTVKEDHILDVKNIIVATGSEVTPFPGIEIDEEKIVSSTGALSLKEIPKRLTIIGGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFKLSTKVISAKRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLEVDKRGRLVIDDQFNSKFPHIKVVGDVTFGPMLAHKAEEEGIAAVEMLKTGHGHVNYNNIPSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAANSRAKTNQDTEGFVKILIDSKTERILGAHIIGPNAGEMIAEAGLALEYGASAEDVARVCHAHPTLSEAFKEANMAAYDKAIHC"},{"created_at":"2011-05-27T02:46:14.000Z","updated_at":"2011-05-27T15:01:18.000Z","name":"2-oxoglutarate dehydrogenase, mitochondrial","uniprot_id":"P20967","uniprot_name":"ODO1_YEAST","enzyme":true,"transporter":false,"gene_name":"KGD1","num_residues":1014,"molecular_weight":"114416.0","theoretical_pi":"7.23","general_function":"Involved in oxoglutarate dehydrogenase (succinyl-transferring) activity","specific_function":"The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components:2- oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3)","reactions":[{"id":2693,"direction":"\u003e","locations":"Mitochondrion matrix. Mitochondrion matrix, mitochondrion nucleoid","altext":"2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2).","export":false,"pw_reaction_id":null,"source":null},{"id":3699,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R003282","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion matrix. Mitochondrion matrix, mitochondrion nucleoid","genbank_gene_id":"M26390","genbank_protein_id":"171785","gene_card_id":"KGD1","chromosome_location":"chromosome 9","locus":"YIL125W","synonyms":["2-oxoglutarate dehydrogenase complex component E1","OGDC-E1","Alpha-ketoglutarate dehydrogenase"],"enzyme_classes":["1.2.4.2"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxoglutarate dehydrogenase (succinyl-transferring) activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" vitamin binding"},{"category":"Function","description":" thiamin pyrophosphate binding"},{"category":"Function","description":" oxidoreductase activity, acting on the aldehyde or oxo group of donors"},{"category":"Function","description":" oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" alcohol metabolic process"},{"category":"Process","description":" monosaccharide metabolic process"},{"category":"Process","description":" hexose metabolic process"},{"category":"Process","description":" glucose metabolic process"},{"category":"Process","description":" glucose catabolic process"},{"category":"Process","description":" glycolysis"}],"pfams":[{"name":"Transket_pyr","identifier":"PF02779"},{"name":"E1_dh","identifier":"PF00676"}],"pathways":[{"name":"Citrate cycle (TCA cycle)","kegg_map_id":"00020"},{"name":"Lysine degradation","kegg_map_id":"00310"},{"name":"Tryptophan metabolism","kegg_map_id":"00380"},{"name":"TCA Cycle","kegg_map_id":null}],"gene_sequence":"ATGCTAAGGTTCGTGTCTTCGCAAACCTGCCGGTATAGTTCAAGAGGACTATTAAAAACATCTTTACTTAAAAATGCATCTACTGTCAAAATTGTCGGAAGAGGGTTAGCCACCACTGGTACAGATAATTTTCTATCGACATCAAATGCCACCTATATCGATGAAATGTACCAAGCTTGGCAAAAAGACCCATCTTCAGTCCATGTTTCATGGGACGCATATTTCAAGAATATGTCTAACCCAAAGATTCCAGCTACAAAGGCTTTTCAGGCTCCTCCCAGTATCAGTAACTTTCCCCAGGGTACCGAAGCAGCTCCCTTAGGGACCGCAATGACTGGTTCAGTAGATGAGAACGTCTCCATTCATCTAAAAGTGCAATTGCTATGTAGAGCTTACCAAGTTAGAGGTCATTTAAAAGCCCATATAGATCCTTTAGGGATCTCATTTGGTAGTAATAAAAATAACCCTGTTCCTCCGGAATTGACTCTAGACTACTACGGCTTTAGCAAACACGATCTTGATAAAGAAATCAACCTAGGACCTGGTATCCTGCCAAGGTTTGCAAGGGACGGGAAATCTAAAATGTCTCTGAAAGAGATTGTGGATCATCTAGAAAAGTTATATTGTTCCTCTTATGGGGTACAATACACACATATTCCATCTAAGCAAAAGTGTGATTGGTTAAGAGAGAGAATTGAGATTCCTGAACCTTACCAATATACAGTGGACCAAAAGAGACAAATCTTAGATAGATTAACATGGGCCACTTCTTTTGAGTCATTCTTATCTACAAAATTTCCAAATGATAAGAGGTTCGGTTTAGAAGGTTTGGAAAGTGTTGTTCCAGGTATTAAAACTTTGGTTGATCGTTCTGTTGAATTGGGTGTAGAAGATATTGTTTTGGGTATGGCTCACCGTGGTAGATTGAACGTTTTATCCAATGTGGTCCGTAAACCAAATGAATCTATTTTTCTGAATTTAAAGGGTTCGAGCGCTCGCGATGATATTGAAGGATCGGGTGATGTCAAGTACCATTTGGGTATGAACTACCAAAGACCAACTACGTCTGGTAAGTACGTCAATTTATCGCTGGTGGCAAATCCTTCTCATTTAGAATCCCAAGATCCAGTTGTTCTTGGTAGAACTAGAGCTTTATTGCATGCCAAGAACGATTTGAAGGAAAAAACAAAGGCCTTAGGTGTGTTATTACATGGTGATGCTGCTTTTGCTGGGCAGGGTGTTGTTTATGAAACCATGGGTTTCTTGACCCTACCAGAATACTCTACTGGTGGTACTATTCATGTTATTACAAACAACCAGATCGGATTCACTACGGATCCAAGATTTGCAAGGTCCACACCATATCCTTCCGATTTGGCTAAGGCCATTGATGCCCCAATTTTCCATGTTAACGCTAATGACGTGGAAGCTGTGACCTTTATTTTCAATTTAGCCGCAGAATGGAGACATAAGTTCCACACAGATGCCATAATTGATGTCGTTGGTTGGAGAAAACATGGACATAATGAAACCGATCGACCATCGTTTACTCAACCATTAATGTACAAAAAAATTGCAAAACAAAAATCTGTCATTGACGTCTATACGGAAAAATTGATAAGTGAAGGCACATTTTCTAAAAAAGATATTGATGAGCACAAGAAATGGGTATGGAACTTATTTGAAGATGCTTTCGAAAAGACAAAGGATTACGTCCCATCTCAAAGAGAATGGTTAACTGCTGCCTGGGAAGGATTCAAATCCCCAAAGGAATTGGCCACTGAGATATTACCACATGAACCAACTAATGTTCCAGAGAGTACTTTGAAAGAACTAGGTAAGGTACTCTCTTCGTGGCCAGAAGGTTTTGAAGTGCACAAAAATCTAAAGAGAATTTTGAAAAATAGAGGAAAATCTATTGAGACAGGTGAAGGCATCGATTGGGCCACCGGTGAAGCATTAGCGTTCGGTACATTGGTTTTGGATGGTCAGAACGTTAGGGTTTCCGGTGAAGATGTAGAAAGAGGTACATTTTCTCAACGTCATGCAGTCTTGCATGACCAACAATCTGAAGCCATTTACACACCGCTAAGCACTCTGAATAATGAAAAGGCAGACTTCACCATTGCAAATTCCTCGTTATCTGAGTACGGTGTAATGGGTTTCGAATATGGTTATTCGCTAACCTCCCCAGATTATCTAGTCATGTGGGAGGCTCAATTCGGTGACTTTGCAAATACAGCACAGGTTATTATTGACCAATTTATTGCCGGTGGTGAACAAAAATGGAAGCAACGCTCTGGTTTAGTTTTGTCTTTACCCCATGGTTATGATGGCCAGGGGCCAGAACATTCGTCTGGTAGATTGGAAAGATTCTTGCAACTAGCCAATGAAGACCCAAGATATTTCCCATCTGAAGAAAAGCTACAGAGACAACATCAGGATTGTAATTTCCAGGTTGTTTATCCAACTACGCCTGCTAATTTATTCCACATTCTAAGGAGACAGCAACATCGTCAATTCCGTAAACCATTGGCGTTATTCTTTTCTAAACAGCTGCTGCGTCACCCATTGGCCAGATCATCTCTTTCCGAATTCACTGAAGGCGGATTCCAATGGATTATCGAAGATATTGAACATGGAAAAAGTATTGGTACGAAAGAGGAAACCAAGAGATTAGTTTTGCTGAGTGGCCAAGTGTACACTGCCCTACATAAAAGACGTGAAAGTTTGGGTGATAAGACCACTGCTTTCTTAAAGATTGAACAGCTGCACCCATTCCCATTTGCTCAGCTACGTGATTCATTAAATTCTTATCCAAACTTGGAAGAAATTGTTTGGTGCCAGGAAGAGCCATTGAACATGGGTTCGTGGGCATACACAGAACCACGCTTACACACAACATTAAAAGAAACGGATAAATATAAGGATTTCAAGGTCAGATACTGTGGTAGAAACCCAAGTGGTGCTGTTGCTGCCGGTAGCAAATCACTACATTTGGCCGAAGAAGATGCCTTTTTGAAAGATGTTTTCCAACAATCCTAA","protein_sequence":"MLRFVSSQTCRYSSRGLLKTSLLKNASTVKIVGRGLATTGTDNFLSTSNATYIDEMYQAWQKDPSSVHVSWDAYFKNMSNPKIPATKAFQAPPSISNFPQGTEAAPLGTAMTGSVDENVSIHLKVQLLCRAYQVRGHLKAHIDPLGISFGSNKNNPVPPELTLDYYGFSKHDLDKEINLGPGILPRFARDGKSKMSLKEIVDHLEKLYCSSYGVQYTHIPSKQKCDWLRERIEIPEPYQYTVDQKRQILDRLTWATSFESFLSTKFPNDKRFGLEGLESVVPGIKTLVDRSVELGVEDIVLGMAHRGRLNVLSNVVRKPNESIFSEFKGSSARDDIEGSGDVKYHLGMNYQRPTTSGKYVNLSLVANPSHLESQDPVVLGRTRALLHAKNDLKEKTKALGVLLHGDAAFAGQGVVYETMGFLTLPEYSTGGTIHVITNNQIGFTTDPRFARSTPYPSDLAKAIDAPIFHVNANDVEAVTFIFNLAAEWRHKFHTDAIIDVVGWRKHGHNETDQPSFTQPLMYKKIAKQKSVIDVYTEKLISEGTFSKKDIDEHKKWVWNLFEDAFEKAKDYVPSQREWLTAAWEGFKSPKELATEILPHEPTNVPESTLKELGKVLSSWPEGFEVHKNLKRILKNRGKSIETGEGIDWATGEALAFGTLVLDGQNVRVSGEDVERGTFSQRHAVLHDQQSEAIYTPLSTLNNEKADFTIANSSLSEYGVMGFEYGYSLTSPDYLVMWEAQFGDFANTAQVIIDQFIAGGEQKWKQRSGLVLSLPHGYDGQGPEHSSGRLERFLQLANEDPRYFPSEEKLQRQHQDCNFQVVYPTTPANLFHILRRQQHRQFRKPLALFFSKQLLRHPLARSSLSEFTEGGFQWIIEDIEHGKSIGTKEETKRLVLLSGQVYTALHKRRESLGDKTTAFLKIEQLHPFPFAQLRDSLNSYPNLEEIVWCQEEPLNMGSWAYTEPRLHTTLKETDKYKDFKVRYCGRNPSGAVAAGSKSLHLAEEDAFLKDVFQQS"}]}