2.0 2012-07-30 14:54:43 -0600 2015-06-03 17:20:47 -0600 ECMDB21164 M2MDB001573 2-Oxepin-2(3H)-ylideneacetyl-CoA 2-Oxepin-2(3h)-ylideneacetyl-CoA is a member of the chemical class known as Coenzyme A and Derivatives. These are derivative of vitamin B5 containing a 4'-phosphopantetheine moiety attached to a diphospho-adenosine. Oxepin-CoA C29H42N7O18P3S 901.666 901.151987801 {[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-2-({[({[(3R)-3-[(2-{[2-({2-[(2Z)-2,3-dihydrooxepin-2-ylidene]acetyl}sulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-3-hydroxy-2,2-dimethylpropoxy](hydroxy)phosphoryl}oxy)(hydroxy)phosphoryl]oxy}methyl)-4-hydroxyoxolan-3-yl]oxy}phosphonic acid oxepin-CoA O[C@H](C(C)(C)COP(=O)(O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)C(=O)NCCC(=O)NCCSC(=O)\C=C1\CC=CC=CO1 InChI=1S/C29H42N7O18P3S/c1-29(2,24(40)27(41)32-8-7-19(37)31-9-11-58-20(38)12-17-6-4-3-5-10-49-17)14-51-57(47,48)54-56(45,46)50-13-18-23(53-55(42,43)44)22(39)28(52-18)36-16-35-21-25(30)33-15-34-26(21)36/h3-5,10,12,15-16,18,22-24,28,39-40H,6-9,11,13-14H2,1-2H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/b17-12-/t18-,22-,23-,24+,28-/m1/s1 ZQZCWPBSHHYCMM-BETJHJQZSA-N Cytosol logp 0.23 ALOGPS logs -2.52 ALOGPS solubility 2.73e+00 g/l ALOGPS logp -5.8 ChemAxon pka_strongest_acidic 0.83 ChemAxon pka_strongest_basic 4.95 ChemAxon iupac {[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-2-({[({[(3R)-3-[(2-{[2-({2-[(2Z)-2,3-dihydrooxepin-2-ylidene]acetyl}sulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-3-hydroxy-2,2-dimethylpropoxy](hydroxy)phosphoryl}oxy)(hydroxy)phosphoryl]oxy}methyl)-4-hydroxyoxolan-3-yl]oxy}phosphonic acid ChemAxon average_mass 901.666 ChemAxon mono_mass 901.151987801 ChemAxon smiles O[C@H](C(C)(C)COP(=O)(O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)C(=O)NCCC(=O)NCCSC(=O)\C=C1\CC=CC=CO1 ChemAxon formula C29H42N7O18P3S ChemAxon inchi InChI=1S/C29H42N7O18P3S/c1-29(2,24(40)27(41)32-8-7-19(37)31-9-11-58-20(38)12-17-6-4-3-5-10-49-17)14-51-57(47,48)54-56(45,46)50-13-18-23(53-55(42,43)44)22(39)28(52-18)36-16-35-21-25(30)33-15-34-26(21)36/h3-5,10,12,15-16,18,22-24,28,39-40H,6-9,11,13-14H2,1-2H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/b17-12-/t18-,22-,23-,24+,28-/m1/s1 ChemAxon inchikey ZQZCWPBSHHYCMM-BETJHJQZSA-N ChemAxon polar_surface_area 372.86 ChemAxon refractivity 202.61 ChemAxon polarizability 79.7 ChemAxon rotatable_bond_count 21 ChemAxon acceptor_count 18 ChemAxon donor_count 9 ChemAxon physiological_charge -4 ChemAxon formal_charge 0 ChemAxon Benzoate degradation via CoA ligation ec00632 Butanoate metabolism ec00650 Phenylalanine metabolism The pathways of the metabolism of phenylalaline begins with the conversion of chorismate to prephenate through a P-protein (chorismate mutase:pheA). Prephenate then interacts with a hydrogen ion through the same previous enzyme resulting in a release of carbon dioxide, water and a phenolpyruvic acid. Three enzymes those enconde by tyrB, aspC and ilvE are involved in catalyzing the third step of these pathways, all three can contribute to the synthesis of phenylalanine: only tyrB and aspC contribute to biosynthesis of tyrosine. Phenolpyruvic acid can also be obtained from a reversivle reaction with ammonia, a reduced acceptor and a D-amino acid dehydrogenase, resulting in a water, an acceptor and a D-phenylalanine, which can be then transported into the periplasmic space by aromatic amino acid exporter. L-phenylalanine also interacts in two reversible reactions, one involved with oxygen through a catalase peroxidase resulting in a carbon dioxide and 2-phenylacetamide. The other reaction involved an interaction with oxygen through a phenylalanine aminotransferase resulting in a oxoglutaric acid and phenylpyruvic acid. L-phenylalanine can be imported into the cytoplasm through an aromatic amino acid:H+ symporter AroP. The compound can also be imported into the periplasmic space through a transporter: L-amino acid efflux transporter. PW000921 ec00360 Metabolic Tryptophan metabolism The biosynthesis of L-tryptophan begins with L-glutamine interacting with a chorismate through a anthranilate synthase which results in a L-glutamic acid, a pyruvic acid, a hydrogen ion and a 2-aminobenzoic acid. The aminobenzoic acid interacts with a phosphoribosyl pyrophosphate through an anthranilate synthase component II resulting in a pyrophosphate and a N-(5-phosphoribosyl)-anthranilate. The latter compound is then metabolized by an indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase resulting in a 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate. This compound then interacts with a hydrogen ion through a indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase resulting in the release of carbon dioxide, a water molecule and a (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate. The latter compound then interacts with a D-glyceraldehyde 3-phosphate and an Indole. The indole interacts with an L-serine through a tryptophan synthase, β subunit dimer resulting in a water molecule and an L-tryptophan. The metabolism of L-tryptophan starts with L-tryptophan being dehydrogenated by a tryptophanase / L-cysteine desulfhydrase resulting in the release of a hydrogen ion, an Indole and a 2-aminoacrylic acid. The latter compound is isomerized into a 2-iminopropanoate. This compound then interacts with a water molecule and a hydrogen ion spontaneously resulting in the release of an Ammonium and a pyruvic acid. The pyruvic acid then interacts with a coenzyme A through a NAD driven pyruvate dehydrogenase complex resulting in the release of a NADH, a carbon dioxide and an Acetyl-CoA PW000815 ec00380 Metabolic beta-Alanine metabolism The Beta-Alanine Metabolism starts with a product of Aspartate metabolism. Aspartate is decarboxylated by aspartate 1-decarboxylase, releasing carbon dioxide and Beta-alanine. Beta alanine is then metabolized through a pantothenate synthetase resulting in Pantothenic acid undergoes phosphorylation through a ATP driven pantothenate kinase, resulting in D-4-phosphopantothenate. Pantothenate (vitamin B5) is the universal precursor for the synthesis of the 4'-phosphopantetheine moiety of coenzyme A and acyl carrier protein. Only plants and microorganismscan synthesize pantothenate de novo - animals require a dietary supplement. The enzymes of this pathway are therefore considered to be antimicrobial drug targets. PW000896 ec00410 Metabolic Propanoate metabolism Starting from L-threonine, this compound is deaminated through a threonine deaminase resulting in a hydrogen ion, a water molecule and a (2z)-2-aminobut-2-enoate. The latter compound then isomerizes to a 2-iminobutanoate, This compound then reacts spontaneously with hydrogen ion and a water molecule resulting in a ammonium and a 2-Ketobutyric acid. The latter compound interacts with CoA through a pyruvate formate-lyase / 2-ketobutyrate formate-lyase resulting in a formic acid and a propionyl-CoA. Propionyl-CoA can then be processed either into a 2-methylcitric acid or into a propanoyl phosphate. Propionyl-CoA interacts with oxalacetic acid and a water molecule through a 2-methylcitrate synthase resulting in a hydrogen ion, a CoA and a 2-Methylcitric acid.The latter compound is dehydrated through a 2-methylcitrate dehydratase resulting in a water molecule and cis-2-methylaconitate. The latter compound is then dehydrated by a bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase resulting in a water molecule and methylisocitric acid. The latter compound is then processed by 2-methylisocitrate lyase resulting in a release of succinic acid and pyruvic acid. Succinic acid can then interact with a propionyl-CoA through a propionyl-CoA:succinate CoA transferase resulting in a propionic acid and a succinyl CoA. Succinyl-CoA is then isomerized through a methylmalonyl-CoA mutase resulting in a methylmalonyl-CoA. This compound is then decarboxylated through a methylmalonyl-CoA decarboxylase resulting in a release of Carbon dioxide and Propionyl-CoA. ropionyl-CoA interacts with a phosphate through a phosphate acetyltransferase / phosphate propionyltransferase resulting in a CoA and a propanoyl phosphate. Propionyl-CoA can react with a phosphate through a phosphate acetyltransferase / phosphate propionyltransferase resulting in a CoA and a propanoyl phosphate. The latter compound is then dephosphorylated through a ADP driven acetate kinase/propionate kinase protein complex resulting in an ATP and Propionic acid. Propionic acid can be processed by a reaction with CoA through a ATP-driven propionyl-CoA synthetase resulting in a pyrophosphate, an AMP and a propionyl-CoA. PW000940 ec00640 Metabolic alpha-Linolenic acid metabolism ec00592 Lysine degradation ec00310 Valine, leucine and isoleucine degradation ec00280 Biosynthesis of unsaturated fatty acids ec01040 Fatty acid elongation in mitochondria ec00062 Fatty acid metabolism This pathway depicts the degradation of palmitic acid (C16:0). Fatty acid degradation and synthesis are relatively simple processes that are essentially the reverse of each other. The process of fatty acid degradation, also known as Beta-Oxidation, converts an aliphatic compound into a set of activated acetyl units (acetyl CoA) that can be processed by the citric acid cycle. An activated fatty acid is first oxidized to introduce a double bond; the double bond is then hydrated to introduce an oxygen; the alcohol is then oxidized to a ketone; and, finally, the four carbon fragment is cleaved by coenzyme A to yield acetyl CoA and a fatty acid chain two carbons shorter. If the fatty acid has an even number of carbon atoms and is saturated, the process is simply repeated until the fatty acid is completely converted into acetyl CoA units. Fatty acid synthesis is essentially the reverse of this process. Because the result is a polymer, the process starts with monomers—in this case with activated acyl group and malonyl units. The malonyl unit is condensed with the acetyl unit to form a four-carbon fragment. To produce the required hydrocarbon chain, the carbonyl must be reduced. The fragment is reduced, dehydrated, and reduced again, exactly the opposite of degradation, to bring the carbonyl group to the level of a methylene group with the formation of butyryl CoA. Another activated malonyl group condenses with the butyryl unit and the process is repeated until a C16 fatty acid is synthesized. The first step converts the hydroxydecanoyl into a trans 2decenoyl acp through a protein complex conformed of a hydroxomyristoyl dehydratase and a hydroxydecanoyl dehydratase. The second step leads to the production of a cis 3 decenoyl acp through a 3-hydroxydecanoyl acp dehydratase. For the third step the cis 3 decenoyl acp enters a cycle involving a synthase, reductase, dehydratase and an enoyl reductase which in turn produce a cis x enoyl-acp, hydroxy cis x enoyl, trans x-2 cis x enoyl acp and cis x enoyl respectively.This is done until a palmitoleoyl is produce. In said case the pathway procedes in two different directions. It can either produce a palmitoleic acid through a acyl-coa thioesterase, or produce a Vaccenic acid through a different set of reactions. This process is achieved through a 3-oxoacyl acp synthase, a 3-oxoacyl acp reductase, a 3r hydroxymyristoyl dehydratase and an enoyl acp reductase that produces a transition through 3-oxo cis vaccenoyl acp, 3 hydroxy cis vaccenoyl acp, cis vaccen 2 enoyl acp and a cis vaccenoyl acp respectively. At this point it goes through one final reaction to produce a Vaccenic acid, through an acyl-CoA thioesterase PW000796 ec00071 Metabolic Geraniol degradation ec00281 Limonene and pinene degradation ec00903 Caprolactam degradation ec00930 Microbial metabolism in diverse environments ec01120 Collection of Reactions without pathways PW001891 Metabolic Phenylethylamine metabolism The process of phenylethylamine metabolism starts with 2-phenylethylamine interacting with an oxygen molecule and a water molecule in the periplasmic space through a phenylethylamine oxidase. This reaction results in the release of a hydrogen peroxide, ammonium and phenylacetaldehyde. Phenylacetaldehyde is introduced into the cytosol and degraded into phenylacetate by reaction with a phenylacetaldehyde dehydrogenase. This reaction involves phenylacetaldehyde interacting with NAD, and a water molecule and then resulting in the release of NADH, and 2 hydrogen ion. Phenylacetate is then degraded. The first step involves phenylacetate interacting with an coenzyme A and an ATP driven phenylacetate-CoA ligase resulting in the release of a AMP, a diphosphate and a phenylacetyl-CoA. This resulting compound the interacts with a hydrogen ion, NADPH, and oxygen molecule through a ring 1,2-phenylacetyl-CoA epoxidase protein complex resulting in the release of a water molecule, an NADP and a 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA. This compound is then metabolized by a ring 1,2 epoxyphenylacetyl-CoA isomerase resulting in a 2-oxepin-2(3H)-ylideneacetyl-CoA. This compound is then hydrolated through a oxepin-CoA hydrolase resulting in a 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde. This commpound then interacts with a water molecule and NADP driven 3-oxo-5,6-dehydrosuberyl-CoA semialadehyde dehydrogenase resulting in 2 hydrogen ions, a NADPH and a 3-oxo-5,6-didehydrosuberyl-CoA. The resulting compound interacts with a coenzyme A and a 3-oxo-5,6 dehydrosuberyl-CoA thiolase resulting in an acetyl-CoA and a 2,3-didehydroadipyl-CoA. This resulting compound is the hydrated by a 2,3-dehydroadipyl-CoA hydratas resulting in a 3-hydroxyadipyl-CoA whuch is dehydrogenated through an NAD driven 3-hydroxyadipyl-CoA dehydrogenase resulting in a NADH, a hydrogen ion and a 3-oxoadipyl-CoA. The latter compound then interacts with conezyme A through a beta-ketoadipyl-CoA thiolase resulting in an acetyl-CoA and a succinyl-CoA. The succinyl-CoA is then integrated into the TCA cycle. PW002027 Metabolic phenylacetate degradation I (aerobic) PWY0-321 Specdb::EiMs 4336 Specdb::NmrOneD 313741 Specdb::NmrOneD 313742 Specdb::NmrOneD 313743 Specdb::NmrOneD 313744 Specdb::NmrOneD 313745 Specdb::NmrOneD 313746 Specdb::NmrOneD 313747 Specdb::NmrOneD 313748 Specdb::NmrOneD 313749 Specdb::NmrOneD 313750 Specdb::NmrOneD 313751 Specdb::NmrOneD 313752 Specdb::NmrOneD 313753 Specdb::NmrOneD 313754 Specdb::NmrOneD 313755 Specdb::NmrOneD 313756 Specdb::NmrOneD 313757 Specdb::NmrOneD 313758 Specdb::NmrOneD 313759 Specdb::NmrOneD 313760 Specdb::MsMs 38117 Specdb::MsMs 38118 Specdb::MsMs 38119 Specdb::MsMs 40565 Specdb::MsMs 40566 Specdb::MsMs 40567 53377481 C19975 CPD0-2363 Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Probable enoyl-CoA hydratase paaF P76082 PAAF_ECOLI paaF http://ecmdb.ca/proteins/P76082.xml Probable enoyl-CoA hydratase paaG P77467 PAAG_ECOLI paaG http://ecmdb.ca/proteins/P77467.xml Protein maoC P77455 MAOC_ECOLI maoC http://ecmdb.ca/proteins/P77455.xml 2-Oxepin-2(3H)-ylideneacetyl-CoA + 2 Water + NADP > 3-Oxo-5,6-dehydrosuberyl-CoA +2 Hydrogen ion + NADPH RXN0-6511 Ring 1,2-epoxyphenylacetyl-CoA <> 2-Oxepin-2(3H)-ylideneacetyl-CoA 2-Oxepin-2(3H)-ylideneacetyl-CoA + Water <> 3-Oxo-5,6-dehydrosuberyl-CoA semialdehyde + 3-Oxo-5,6-dehydrosuberyl-CoA semialdehyde R09836 2-(1,2-Epoxy-1,2-dihydrophenyl)acetyl-CoA + 2-(1,2-Epoxy-1,2-dihydrophenyl)acetyl-CoA <> 2-Oxepin-2(3H)-ylideneacetyl-CoA R09837 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA <> 2-Oxepin-2(3H)-ylideneacetyl-CoA RXN0-6510 2-Oxepin-2(3H)-ylideneacetyl-CoA + NADP + Water > 3-Oxo-5,6-dehydrosuberyl-CoA + NADPH + Hydrogen ion RXN0-6511 2-Oxepin-2(3H)-ylideneacetyl-CoA + Water > 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde RXNMETA-12671 2-(1,2-Epoxy-1,2-dihydrophenyl)acetyl-CoA > 2-Oxepin-2(3H)-ylideneacetyl-CoA 2-Oxepin-2(3H)-ylideneacetyl-CoA + Water > 3-Oxo-5,6-dehydrosuberyl-CoA semialdehyde