You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-07-23 05:44:26 UTC
HMDB IDHMDB0000738
Secondary Accession Numbers
  • HMDB00738
Metabolite Identification
Common NameIndole
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 human 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. Indole has been found in Alcaligenes, Aspergillus, Pseudomonas (PMID: 23194589 ; PMID: 2310183 ; PMID: 9680309 ).
Structure
Data?1563860666
Synonyms
ValueSource
2,3-BenzopyrroleChEBI
indolChEBI
1-AzaindeneHMDB
1-BenzazoleHMDB
Benzo[b]pyrroleHMDB
KetoleHMDB
Indole, 14C-labeledHMDB
Indole hydrochlorideHMDB
Chemical FormulaC8H7N
Average Molecular Weight117.1479
Monoisotopic Molecular Weight117.057849229
IUPAC Name1H-indole
Traditional Nameindole
CAS Registry Number120-72-9
SMILES
N1C=CC2=C1C=CC=C2
InChI Identifier
InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H
InChI KeySIKJAQJRHWYJAI-UHFFFAOYSA-N
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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point52.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.56 mg/mLNot Available
LogP2.14HANSCH,C ET AL. (1995)
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
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-6900000000-09af4d0af4e5f7259a59JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-4160749bd673d5e00048JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-33bf321019a6a8e3401aJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-6900000000-09af4d0af4e5f7259a59JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-4160749bd673d5e00048JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-014i-9800000000-33bf321019a6a8e3401aJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-7900000000-2a9e4ccc61fee73a480eJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014i-0900000000-622dfed80152ea08d52aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0006-9100000000-2531cceca05522a5489eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-014l-9000000000-5e07c15293929ff4440fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (MX-1303) , Positivesplash10-014i-6900000000-09af4d0af4e5f7259a59JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-014i-9800000000-4160749bd673d5e00048JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-68) , Positivesplash10-014i-9800000000-33bf321019a6a8e3401aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-014i-0900000000-e6b11e225744a0d85f71JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-014i-0900000000-e6b11e225744a0d85f71JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-7b49c1c370d7355c5e6fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-050ef45f3ec404d7eb65JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-79ff95be504a5efad264JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-31ff8b484e0dc207fcc9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-0006-9000000000-864a48552fea562fc370JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-bd82bfab4567619b5c41JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-6bff353534e6f5f9105bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-0900000000-c4e339d4a1d3fda0a949JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014i-2900000000-100cd0cc67ac9eda3f4eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-014l-5900000000-79447b563349d08aacc0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - ESI-ITFT , positivesplash10-00kf-9800000000-a1ce5da5416e6d003ff9JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0900000000-aba5022e03d31dcbcc86JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-0900000000-78c0f569df5b7f51c52cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-6900000000-bacb6e9a65a688229f96JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-e93b2f48040666dd7fe0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-0900000000-07d8a93ec0ace38ef3b3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-014i-6900000000-8abfc9b162cc93f153acJSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-014i-9700000000-3b1ec48b5bce79adb282JSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Intestine
  • Nerve Cells
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Not SpecifiedNot Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected and Quantified32352.266 nmol/g wet fecesAdult (>18 years old)Not Specified
Normal
details
FecesDetected but not Quantified Children (1-13 years old)BothNormal details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected and Quantified11962.0867 nmol/g wet fecesAdult (>18 years old)Not Specified
Normal
details
FecesDetected but not Quantified Not SpecifiedNot Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected and Quantified23400.619 nmol/g wet fecesAdult (>18 years old)Not Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
FecesDetected but not Quantified Children (1-13 years old)Not Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Not SpecifiedNot Specified
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Newborn (0-30 days old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
SalivaDetected but not Quantified Adult (>18 years old)Not SpecifiedNormal details
UrineDetected but not Quantified Adult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Children (1-13 years old)BothAutism details
FecesDetected but not Quantified Children (1-13 years old)BothPervasive Developmental Disorder Not Otherwise Specified details
FecesDetected but not Quantified Adult (>18 years old)BothCrohns disease details
FecesDetected but not Quantified Adult (>18 years old)Both
Nonalcoholic fatty liver disease (NAFLD)
details
FecesDetected but not Quantified Adult (>18 years old)BothUlcerative colitis details
FecesDetected but not Quantified Adult (>18 years old)Both
Ulcerative colitis
details
FecesDetected but not Quantified Adult (>18 years old)Both
Crohn's disease
details
FecesDetected but not Quantified Not SpecifiedNot Specified
Crohn's disease
details
FecesDetected but not Quantified Not SpecifiedNot Specified
Ulcerative colitis
details
FecesDetected and Quantified0.00108 (0.000478-0.00501) nmol/g wet fecesNot SpecifiedNot Specified
Crohns disease
details
FecesDetected and Quantified0.000230 (0.000111-0.00139) nmol/g wet fecesNot SpecifiedNot Specified
Ulcerative colitis
details
FecesDetected and Quantified0.000350 (0.000068-0.000999) nmol/g wet fecesNot SpecifiedNot Specified
Irritable bowel syndrome
details
FecesDetected but not Quantified Adult (>18 years old)Both
Campylobacter jejuni infection
details
FecesDetected but not Quantified Adult (>18 years old)Both
Clostridium difficile infection
details
FecesDetected but not Quantified Adult (>18 years old)Both
Ulcerative Colitis
details
FecesDetected and Quantified0-132368.285 nmol/g wet fecesChildren (1-13 years old)Not Specified
Treated celiac disease
details
FecesDetected but not Quantified Adult (>18 years old)BothImmunoglobulin A nephropathy (IgAN) non progressor details
FecesDetected but not Quantified Adult (>18 years old)BothImmunoglobulin A nephropathy (IgAN) progressor details
UrineDetected but not Quantified Adult (>18 years old)BothBreast cancer details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
  2. Walton C, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Cole JA, Cauchi M, Bessant C, Hunter JO: Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases. Inflamm Bowel Dis. 2013 Sep;19(10):2069-78. doi: 10.1097/MIB.0b013e31829a91f6. [PubMed:23867873 ]
  3. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
  4. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Celiac disease
  1. Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, Gobbetti M, Francavilla R: Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol. 2011 Oct 4;11:219. doi: 10.1186/1471-2180-11-219. [PubMed:21970810 ]
Crohn's disease
  1. Walton C, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Cole JA, Cauchi M, Bessant C, Hunter JO: Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases. Inflamm Bowel Dis. 2013 Sep;19(10):2069-78. doi: 10.1097/MIB.0b013e31829a91f6. [PubMed:23867873 ]
  2. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
  3. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Irritable bowel syndrome
  1. Walton C, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Cole JA, Cauchi M, Bessant C, Hunter JO: Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases. Inflamm Bowel Dis. 2013 Sep;19(10):2069-78. doi: 10.1097/MIB.0b013e31829a91f6. [PubMed:23867873 ]
Autism
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Pervasive developmental disorder not otherwise specified
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Perillyl alcohol administration for cancer treatment
  1. Silva CL, Passos M, Camara JS: Solid phase microextraction, mass spectrometry and metabolomic approaches for detection of potential urinary cancer biomarkers--a powerful strategy for breast cancer diagnosis. Talanta. 2012 Jan 30;89:360-8. doi: 10.1016/j.talanta.2011.12.041. Epub 2011 Dec 22. [PubMed:22284503 ]
Associated OMIM IDs
DrugBank IDDB04532
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012008
KNApSAcK IDC00001418
Chemspider ID776
KEGG Compound IDC00463
BioCyc IDINDOLE
BiGG IDNot Available
Wikipedia LinkIndole
METLIN ID286
PubChem Compound798
PDB IDNot Available
ChEBI ID16881
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceGrigoleit, Georg; Oberkobusch, Rudolf; Collin, Gerd. Indole from 2-ethylaniline. Ger. Offen. (1973), 6 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. Scott AK: Sumatriptan clinical pharmacokinetics. Clin Pharmacokinet. 1994 Nov;27(5):337-44. [PubMed:7851052 ]
  5. 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 ]
  6. 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 ]
  7. 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 ]
  8. 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 ]
  9. 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 ]
  10. Yoshida M, Mishiro Y: [Indole production in human whole saliva]. Shigaku. 1989 Aug;77(2):472-86. [PubMed:2489307 ]
  11. 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 ]
  12. 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 ]
  13. Raw I, Schmidt BJ, Merzel J: Catecholamines and congenital pain insensitivity. Braz J Med Biol Res. 1984;17(3-4):271-9. [PubMed:6085021 ]
  14. Claus G, Kutzner HJ: Degradation of indole by Alcaligenes spec. Syst Appl Microbiol. 1983;4(2):169-80. doi: 10.1016/S0723-2020(83)80046-0. [PubMed:23194589 ]
  15. Kamath AV, Vaidyanathan CS: New pathway for the biodegradation of indole in Aspergillus niger. Appl Environ Microbiol. 1990 Jan;56(1):275-80. [PubMed:2310183 ]
  16. Doukyu N, Aono R: Biodegradation of indole at high concentration by persolvent fermentation with Pseudomonas sp. ST-200. Extremophiles. 1997 May;1(2):100-5. [PubMed:9680309 ]