2.0 2012-05-31 13:00:55 -0600 2015-09-13 12:56:09 -0600 ECMDB00738 M2MDB000181 Indole Indole is an aromatic heterocyclic organic compound. It has a bicyclic structure, consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. It can be produced by bacteria as a degradation product of the amino acid tryptophan. It occurs naturally in feces and has an intense fecal smell. At very low concentrations, however, it has a flowery smell, and is a constituent of many flower scents (such as orange blossoms) and perfumes. Natural jasmine oil, used in the perfume industry, contains around 2.5% of indole. Indole also occurs in CoAl tar. The participation of the nitrogen lone electron pair in the aromatic ring means that indole is not a base, and it does not behave like a simple amine. 1-Azaindene 1-Benzazole 2,3-Benzopyrrole Benzo[b]pyrrole Indole Ketole C8H7N 117.1479 117.057849229 1H-indole indole 120-72-9 N1C=CC2=C1C=CC=C2 InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N Solid Cytosol Extra-organism Membrane Periplasm logp 2.29 ALOGPS logs -1.34 ALOGPS solubility 5.31e+00 g/l ALOGPS melting_point 52.5 oC logp 2.07 ChemAxon pka_strongest_acidic 16.44 ChemAxon iupac 1H-indole ChemAxon average_mass 117.1479 ChemAxon mono_mass 117.057849229 ChemAxon smiles N1C=CC2=C1C=CC=C2 ChemAxon formula C8H7N ChemAxon inchi InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H ChemAxon inchikey SIKJAQJRHWYJAI-UHFFFAOYSA-N ChemAxon polar_surface_area 15.79 ChemAxon refractivity 37.14 ChemAxon polarizability 12.82 ChemAxon rotatable_bond_count 0 ChemAxon acceptor_count 0 ChemAxon donor_count 1 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Nitrogen metabolism The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction and dissimilatory nitrate reduction both for conversion to ammonia, and denitrification. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere. Nitrate can be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK or a nitrate / nitrite transporter NarU. Nitrate is then reduced by a Nitrate Reductase resulting in the release of water, an acceptor and a Nitrite. Nitrite can also be introduced into the cytoplasm through a nitrate:nitrite antiporter NarK Nitrite can be reduced a NADPH dependent nitrite reductase resulting in water and NAD and Ammonia. Nitrite can interact with hydrogen ion, ferrocytochrome c through a cytochrome c-552 ferricytochrome resulting in the release of ferricytochrome c, water and ammonia Another process by which ammonia is produced is by a reversible reaction of hydroxylamine with a reduced acceptor through a hydroxylamine reductase resulting in an acceptor, water and ammonia. Water and carbon dioxide react through a carbonate dehydratase resulting in carbamic acid. This compound reacts spontaneously with hydrogen ion resulting in the release of carbon dioxide and ammonia. Carbon dioxide can interact with water through a carbonic anhydrase resulting in hydrogen carbonate. This compound interacts with cyanate and hydrogen ion through a cyanate hydratase resulting in a carbamic acid. Ammonia can be metabolized by reacting with L-glutamine and ATP driven glutamine synthetase resulting in ADP, phosphate and L-glutamine. The latter compound reacts with oxoglutaric acid and hydrogen ion through a NADPH dependent glutamate synthase resulting in the release of NADP and L-glutamic acid. L-glutamic acid reacts with water through a NADP-specific glutamate dehydrogenase resulting in the release of oxoglutaric acid, NADPH, hydrogen ion and ammonia. PW000755 ec00910 Metabolic Phenylalanine, tyrosine and tryptophan biosynthesis ec00400 Glycine, serine and threonine metabolism ec00260 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 Metabolic pathways eco01100 tryptophan metabolism II 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 PW001916 Metabolic tryptophan degradation II (via pyruvate) TRYPDEG-PWY tryptophan biosynthesis TRPSYN-PWY Specdb::CMs 2683 Specdb::CMs 27171 Specdb::CMs 27342 Specdb::CMs 27536 Specdb::CMs 99600 Specdb::CMs 99601 Specdb::CMs 99602 Specdb::CMs 148814 Specdb::EiMs 319 Specdb::NmrOneD 1511 Specdb::NmrOneD 2184 Specdb::NmrOneD 2875 Specdb::NmrOneD 5138 Specdb::NmrOneD 5139 Specdb::MsMs 1047 Specdb::MsMs 1048 Specdb::MsMs 1049 Specdb::MsMs 4590 Specdb::MsMs 4591 Specdb::MsMs 4592 Specdb::MsMs 4593 Specdb::MsMs 182706 Specdb::MsMs 182707 Specdb::MsMs 182708 Specdb::MsMs 183054 Specdb::MsMs 183055 Specdb::MsMs 183056 Specdb::MsMs 447947 Specdb::MsMs 448373 Specdb::MsMs 448374 Specdb::MsMs 448375 Specdb::MsMs 448376 Specdb::MsMs 448377 Specdb::MsMs 448378 Specdb::MsMs 448379 Specdb::MsMs 448380 Specdb::MsMs 448381 Specdb::MsMs 448382 Specdb::MsMs 448383 Specdb::NmrTwoD 1035 Specdb::NmrTwoD 1457 HMDB00738 798 776 C00463 16881 INDOLE IND Indole Keseler, I. 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(1973), 6 pp. http://hmdb.ca/system/metabolites/msds/000/000/657/original/HMDB00738.pdf?1358894583 Tryptophanase P0A853 TNAA_ECOLI tnaA http://ecmdb.ca/proteins/P0A853.xml Tryptophan synthase alpha chain P0A877 TRPA_ECOLI trpA http://ecmdb.ca/proteins/P0A877.xml Tryptophan synthase beta chain P0A879 TRPB_ECOLI trpB http://ecmdb.ca/proteins/P0A879.xml Tryptophan-specific transport protein P0AAD2 MTR_ECOLI mtr http://ecmdb.ca/proteins/P0AAD2.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Outer membrane pore protein E P02932 PHOE_ECOLI phoE http://ecmdb.ca/proteins/P02932.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Acriflavine resistance protein F P24181 ACRF_ECOLI acrF http://ecmdb.ca/proteins/P24181.xml Outer membrane protein tolC P02930 TOLC_ECOLI tolC http://ecmdb.ca/proteins/P02930.xml Acriflavine resistance protein E P24180 ACRE_ECOLI acrE http://ecmdb.ca/proteins/P24180.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml Indole + L-Serine > Water + L-Tryptophan R00674 RXN0-2382 Indoleglycerol phosphate > D-Glyceraldehyde 3-phosphate + Indole R02340 RXN0-2381 Water + L-Tryptophan <> Indole + Ammonium + Pyruvic acid L-Tryptophan + Water <> Indole + Pyruvic acid + Ammonia R00673 TRYPTOPHAN-RXN L-Serine + Indole <> L-Tryptophan + Water R00674 Indoleglycerol phosphate <> Indole + D-Glyceraldehyde 3-phosphate R02340 L-Tryptophan + Water <> Hydrogen ion + Indole + Pyruvic acid + Ammonia TRYPTOPHAN-RXN L-Tryptophan + Water > Indole + Pyruvic acid + Ammonia L-Tryptophan + Water + 2-Aminoacrylic acid + 2-Iminopropanoate <> Indole + Pyruvic acid + Ammonia R00673 L-Serine + Indoleglycerol phosphate + Indole <> L-Tryptophan + D-Glyceraldehyde 3-phosphate + Water R02722 (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate > D-Glyceraldehyde 3-phosphate + Indole + D-Glyceraldehyde 3-phosphate PW_R002899 Indole + L-Serine + L-Serine > Water + L-Tryptophan PW_R002900 L-Tryptophan > Hydrogen ion + Indole + 2-Aminoacrylic acid PW_R002901 Indole + L-Serine > Water + L-Tryptophan Indole + L-Serine > Water + L-Tryptophan L-Serine + Indole <> L-Tryptophan + Water