Record Information
Version2.0
Creation Date2012-05-31 13:00:55 -0600
Update Date2015-09-13 12:56:09 -0600
Secondary Accession Numbers
  • ECMDB00738
Identification
Name:Indole
DescriptionIndole 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.
Structure
Thumb
Synonyms:
  • 1-Azaindene
  • 1-Benzazole
  • 2,3-Benzopyrrole
  • Benzo[b]pyrrole
  • Indole
  • Ketole
Chemical Formula:C8H7N
Weight:Average: 117.1479
Monoisotopic: 117.057849229
InChI Key:SIKJAQJRHWYJAI-UHFFFAOYSA-N
InChI:InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H
CAS number:120-72-9
IUPAC Name:1H-indole
Traditional IUPAC Name:indole
SMILES:N1C=CC2=C1C=CC=C2
Chemical Taxonomy
Description belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassIndoles
Direct ParentIndoles
Alternative Parents
Substituents
  • Indole
  • Benzenoid
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:52.5 °C
Experimental Properties:
PropertyValueSource
Water Solubility:3.56 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP:2.14 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility5.31 g/LALOGPS
logP2.29ALOGPS
logP2.07ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)16.44ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area15.79 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.14 m³·mol⁻¹ChemAxon
Polarizability12.82 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Nitrogen metabolismPW000755 ThumbThumb?image type=greyscaleThumb?image type=simple
Tryptophan metabolismPW000815 ThumbThumb?image type=greyscaleThumb?image type=simple
tryptophan metabolism IIPW001916 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-6900000000-09af4d0af4e5f7259a59View in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-4160749bd673d5e00048View in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-33bf321019a6a8e3401aView in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-6900000000-09af4d0af4e5f7259a59View in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-4160749bd673d5e00048View in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-33bf321019a6a8e3401aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-7900000000-2a9e4ccc61fee73a480eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014i-0900000000-622dfed80152ea08d52aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0006-9100000000-2531cceca05522a5489eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-014l-9000000000-5e07c15293929ff4440fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (MX-1303) , Positivesplash10-014i-6900000000-09af4d0af4e5f7259a59View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-014i-9800000000-4160749bd673d5e00048View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-68) , Positivesplash10-014i-9800000000-33bf321019a6a8e3401aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-014i-0900000000-e6b11e225744a0d85f71View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-014i-0900000000-e6b11e225744a0d85f71View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-7b49c1c370d7355c5e6fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-050ef45f3ec404d7eb65View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-79ff95be504a5efad264View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-31ff8b484e0dc207fcc9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-864a48552fea562fc370View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-bd82bfab4567619b5c41View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-6bff353534e6f5f9105bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-c4e339d4a1d3fda0a949View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-2900000000-100cd0cc67ac9eda3f4eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014l-5900000000-79447b563349d08aacc0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-00kf-9800000000-a1ce5da5416e6d003ff9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0900000000-aba5022e03d31dcbcc86View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-0900000000-78c0f569df5b7f51c52cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-6900000000-bacb6e9a65a688229f96View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-e93b2f48040666dd7fe0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-0900000000-07d8a93ec0ace38ef3b3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-014i-6900000000-8abfc9b162cc93f153acView in MoNA
MSMass Spectrum (Electron Ionization)splash10-014i-9700000000-3b1ec48b5bce79adb282View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Agatsuma S, Sekino H, Watanabe H: Indoxyl-beta-D-glucuronide and 3-indoxyl sulfate in plasma of hemodialysis patients. Clin Nephrol. 1996 Apr;45(4):250-6. Pubmed: 8861801
  • Aoyama I, Miyazaki T, Niwa T: Preventive effects of an oral sorbent on nephropathy in rats. Miner Electrolyte Metab. 1999 Jul-Dec;25(4-6):365-72. Pubmed: 10681668
  • Citron DM, Baron EJ, Finegold SM, Goldstein EJ: Short prereduced anaerobically sterilized (PRAS) biochemical scheme for identification of clinical isolates of bile-resistant Bacteroides species. J Clin Microbiol. 1990 Oct;28(10):2220-3. Pubmed: 2229345
  • Cooke M, Leeves N, White C: Time profile of putrescine, cadaverine, indole and skatole in human saliva. Arch Oral Biol. 2003 Apr;48(4):323-7. Pubmed: 12663078
  • Coowar D, Bouissac J, Hanbali M, Paschaki M, Mohier E, Luu B: Effects of indole fatty alcohols on the differentiation of neural stem cell derived neurospheres. J Med Chem. 2004 Dec 2;47(25):6270-82. Pubmed: 15566297
  • Freedman DX, Belendiuk K, Belendiuk GW, Crayton JW: Blood tryptophan metabolism in chronic schizophrenics. Arch Gen Psychiatry. 1981 Jun;38(6):655-9. Pubmed: 7247628
  • Gambhir KK, McMenamy RH, Watson F: Positions in human serum albumin which involve the indole binding site. Sequence of 107-residue fragment. J Biol Chem. 1975 Sep 10;250(17):6711-9. Pubmed: 1158878
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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. Pubmed: 21097882
  • Kunka RL, Hussey EK, Shaw S, Warner P, Aubert B, Richard I, Fowler PA, Pakes GE: Safety, tolerability, and pharmacokinetics of sumatriptan suppositories following single and multiple doses in healthy volunteers. Cephalalgia. 1997 Jun;17(4):532-40. Pubmed: 9209775
  • Raw I, Schmidt BJ, Merzel J: Catecholamines and congenital pain insensitivity. Braz J Med Biol Res. 1984;17(3-4):271-9. Pubmed: 6085021
  • Scott AK: Sumatriptan clinical pharmacokinetics. Clin Pharmacokinet. 1994 Nov;27(5):337-44. Pubmed: 7851052
  • Takken W, van Loon JJ, Adam W: Inhibition of host-seeking response and olfactory responsiveness in Anopheles gambiae following blood feeding. J Insect Physiol. 2001 Mar;47(3):303-310. Pubmed: 11119776
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Welch DF, Ahlin PA, Matsen JM: Differentiation of Haemophilus spp. in Respiratory isolate cultures by an indole spot test. J Clin Microbiol. 1982 Feb;15(2):216-9. Pubmed: 7040445
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • Yoshida M, Mishiro Y: [Indole production in human whole saliva] Shigaku. 1989 Aug;77(2):472-86. Pubmed: 2489307
Synthesis Reference:Grigoleit, Georg; Oberkobusch, Rudolf; Collin, Gerd. Indole from 2-ethylaniline. Ger. Offen. (1973), 6 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID16881
HMDB IDHMDB00738
Pubchem Compound ID798
Kegg IDC00463
ChemSpider ID776
WikipediaIndole
BioCyc IDINDOLE
EcoCyc IDINDOLE
Ligand ExpoIND

Enzymes

General function:
Involved in lyase activity
Specific function:
L-tryptophan + H(2)O = indole + pyruvate + NH(3)
Gene Name:
tnaA
Uniprot ID:
P0A853
Molecular weight:
52773
Reactions
L-tryptophan + H(2)O = indole + pyruvate + NH(3).
General function:
Involved in catalytic activity
Specific function:
The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3- phosphate
Gene Name:
trpA
Uniprot ID:
P0A877
Molecular weight:
28724
Reactions
L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H(2)O.
General function:
Involved in catalytic activity
Specific function:
The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine
Gene Name:
trpB
Uniprot ID:
P0A879
Molecular weight:
42983
Reactions
L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H(2)O.

Transporters

General function:
Involved in amino acid transmembrane transporter activity
Specific function:
Involved in transporting tryptophan across the cytoplasmic membrane
Gene Name:
mtr
Uniprot ID:
P0AAD2
Molecular weight:
44332
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Involved in cell envelope formation. Is produced in extremely low amounts
Gene Name:
acrF
Uniprot ID:
P24181
Molecular weight:
111454
General function:
Involved in transporter activity
Specific function:
Required for proper expression of outer membrane protein genes such as ompF, nmpC, protein 2, hemolysin, colicin V, or colicin E1. May be specialized for signal sequence independent, extracellular secretion in Gram-negative bacteria
Gene Name:
tolC
Uniprot ID:
P02930
Molecular weight:
53740
General function:
Involved in transmembrane transport
Specific function:
May affect specific membrane functions, such as septum formation during cell division, and cell membrane permeability
Gene Name:
acrE
Uniprot ID:
P24180
Molecular weight:
41317
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368