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Showing metabocard for Indole (HMDB0000738)

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enzymes (1) Show 1 protein
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:07 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. 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 is a microbial metabolite and 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, indole has a flowery smell and is a constituent of many flower scents (such as orange blossoms) and perfumes. As a volatile organic compound, indole has been identified as a fecal biomarker of Clostridium difficile infection (PMID: 30986230 ). Natural jasmine oil, used in the perfume industry, contains around 2.5% of indole. Indole also occurs in coal tar. Indole has been found to be produced in a number of bacterial genera including Alcaligenes, Aspergillus, Escherichia, and Pseudomonas (PMID: 23194589 , 2310183 , 9680309 ). Indole plays a role in bacterial biofilm formation, bacterial motility, bacterial virulence, plasmid stability, and antibiotic resistance. It also functions as an intercellular signalling molecule (PMID: 26115989 ). Recently, it was determined that the bacterial membrane-bound histidine sensor kinase (HK) known as CpxA acts as a bacterial indole sensor to facilitate signalling (PMID: 31164470 ). It has been found that decreased indole concentrations in the gut promote bacterial pathogenesis, while increased levels of indole in the gut decrease bacterial virulence gene expression (PMID: 31164470 ). As a result, enteric pathogens sense a gradient of indole concentrations in the gut to migrate to different niches and successfully establish an infection.
Structure
Data?1676999707
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000738 (Indole)

Indole.mol
  Mrv1652309042000062D          

  9 10  0  0  0  0            999 V2000
   -0.8643   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3492    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8643    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0797    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3492    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3492   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0797   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  4  9  2  0  0  0  0
M  END
Download

3D MOL for HMDB0000738 (Indole)

HMDB0000738
     RDKit          3D
Indole
 16 17  0  0  0  0  0  0  0  0999 V2000
   -2.0866    0.7054   -0.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0364   -0.6712   -0.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8642   -1.3845    0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3435   -0.6948    0.0611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6153   -1.1125    0.1613 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4099   -0.0360    0.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6263    1.0900    0.0330 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2984    0.6866   -0.0224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8880    1.3898   -0.1342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0353    1.2245   -0.2524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9790   -1.2270   -0.1055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8657   -2.4617    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9610   -2.0892    0.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4811   -0.0151    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9131    2.1238   -0.0104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8933    2.4719   -0.1979 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
M  END
Download

3D SDF for HMDB0000738 (Indole)

Indole.mol
  Mrv1652309042000062D          

  9 10  0  0  0  0            999 V2000
   -0.8643   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3492    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8643    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0797    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3492    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3492   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0797   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  4  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000738

> <DATABASE_NAME>
hmdb

> <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_KEY>
SIKJAQJRHWYJAI-UHFFFAOYSA-N

> <FORMULA>
C8H7N

> <MOLECULAR_WEIGHT>
117.1479

> <EXACT_MASS>
117.057849229

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
12.81574628396194

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indole

> <ALOGPS_LOGP>
2.29

> <JCHEM_LOGP>
2.0720078089999996

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.437037050201045

> <JCHEM_POLAR_SURFACE_AREA>
15.79

> <JCHEM_REFRACTIVITY>
37.1445

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.31e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
indole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0000738 (Indole)

HMDB0000738
     RDKit          3D
Indole
 16 17  0  0  0  0  0  0  0  0999 V2000
   -2.0866    0.7054   -0.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0364   -0.6712   -0.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8642   -1.3845    0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3435   -0.6948    0.0611 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6153   -1.1125    0.1613 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4099   -0.0360    0.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6263    1.0900    0.0330 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2984    0.6866   -0.0224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8880    1.3898   -0.1342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0353    1.2245   -0.2524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9790   -1.2270   -0.1055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8657   -2.4617    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9610   -2.0892    0.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4811   -0.0151    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9131    2.1238   -0.0104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8933    2.4719   -0.1979 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
M  END
Download

PDB for HMDB0000738 (Indole)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Indole.mol                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0      -1.613  -1.246   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -2.519   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.613   1.246   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.149   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.185   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.519   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.519  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.185  -1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.149  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    1    4                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
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3D PDB for HMDB0000738 (Indole)

COMPND    HMDB0000738
HETATM    1  C1  UNL     1      -2.087   0.705  -0.166  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.036  -0.671  -0.082  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.864  -1.384   0.030  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.343  -0.695   0.061  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.615  -1.112   0.161  1.00  0.00           N  
HETATM    6  C5  UNL     1       2.410  -0.036   0.146  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.626   1.090   0.033  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.298   0.687  -0.022  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.888   1.390  -0.134  1.00  0.00           C  
HETATM   10  H1  UNL     1      -3.035   1.225  -0.252  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.979  -1.227  -0.105  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.866  -2.462   0.093  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.961  -2.089   0.239  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.481  -0.015   0.208  1.00  0.00           H  
HETATM   15  H6  UNL     1       1.913   2.124  -0.010  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.893   2.472  -0.198  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    4   12
CONECT    4    5    8
CONECT    5    6   13
CONECT    6    7    7   14
CONECT    7    8   15
CONECT    8    9    9
CONECT    9   16
END
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SMILES for HMDB0000738 (Indole)

N1C=CC2=C1C=CC=C2
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INCHI for HMDB0000738 (Indole)

InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,3-BenzopyrroleChEBI
indolChEBI
1-AzaindeneHMDB
1-BenzazoleHMDB
Benzo[b]pyrroleHMDB
KetoleHMDB
IndoleHMDB
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
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point52.5 °CNot Available
Boiling Point253.00 to 254.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility3.56 mg/mLNot Available
LogP2.14HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg117.08530932474
[M+H]+MetCCS_train_pos120.98630932474
[M-H]-Not Available117.085http://allccs.zhulab.cn/database/detail?ID=AllCCS00000330
[M+H]+Not Available120.856http://allccs.zhulab.cn/database/detail?ID=AllCCS00000330
Predicted Molecular 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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+123.11631661259
DarkChem[M-H]-119.48731661259
AllCCS[M+H]+121.51432859911
AllCCS[M-H]-118.70732859911
DeepCCS[M+H]+122.34530932474
DeepCCS[M-H]-119.93530932474
DeepCCS[M-2H]-156.21930932474
DeepCCS[M+Na]+130.98430932474
AllCCS[M+H]+121.532859911
AllCCS[M+H-H2O]+116.432859911
AllCCS[M+NH4]+126.332859911
AllCCS[M+Na]+127.732859911
AllCCS[M-H]-118.732859911
AllCCS[M+Na-2H]-120.132859911
AllCCS[M+HCOO]-121.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
IndoleN1C=CC2=C1C=CC=C22427.7Standard polar33892256
IndoleN1C=CC2=C1C=CC=C21234.0Standard non polar33892256
IndoleN1C=CC2=C1C=CC=C21309.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Indole,1TMS,isomer #1C[Si](C)(C)N1C=CC2=CC=CC=C211424.0Semi standard non polar33892256
Indole,1TMS,isomer #1C[Si](C)(C)N1C=CC2=CC=CC=C211424.2Standard non polar33892256
Indole,1TMS,isomer #1C[Si](C)(C)N1C=CC2=CC=CC=C211720.5Standard polar33892256
Indole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC2=CC=CC=C211688.3Semi standard non polar33892256
Indole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC2=CC=CC=C211628.0Standard non polar33892256
Indole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC2=CC=CC=C211851.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Indole EI-B (Non-derivatized)splash10-014i-6900000000-09af4d0af4e5f7259a592017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Indole EI-B (Non-derivatized)splash10-014i-9800000000-4160749bd673d5e000482017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Indole EI-B (Non-derivatized)splash10-014i-9800000000-33bf321019a6a8e3401a2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Indole EI-B (Non-derivatized)splash10-014i-6900000000-09af4d0af4e5f7259a592018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Indole EI-B (Non-derivatized)splash10-014i-9800000000-4160749bd673d5e000482018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Indole EI-B (Non-derivatized)splash10-014i-9800000000-33bf321019a6a8e3401a2018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Indole GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-7900000000-2a9e4ccc61fee73a480e2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Indole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-014i-9700000000-3b1ec48b5bce79adb2822014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-014i-0900000000-622dfed80152ea08d52a2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-0006-9100000000-2531cceca05522a5489e2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-014l-9000000000-5e07c15293929ff4440f2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole EI-B (MX-1303) , Positive-QTOFsplash10-014i-6900000000-09af4d0af4e5f7259a592012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole EI-B (Unknown) , Positive-QTOFsplash10-014i-9800000000-4160749bd673d5e000482012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole EI-B (HITACHI M-68) , Positive-QTOFsplash10-014i-9800000000-33bf321019a6a8e3401a2012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive-QTOFsplash10-014i-0900000000-e6b11e225744a0d85f712012-08-31HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole LC-ESI-QTOF , positive-QTOFsplash10-014i-0900000000-e6b11e225744a0d85f712017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-014i-0900000000-7b49c1c370d7355c5e6f2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-0006-9000000000-050ef45f3ec404d7eb652017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-0006-9000000000-79ff95be504a5efad2642017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-0006-9000000000-31ff8b484e0dc207fcc92017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-0006-9000000000-864a48552fea562fc3702017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-014i-0900000000-bd82bfab4567619b5c412017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-014i-0900000000-6bff353534e6f5f9105b2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-014i-0900000000-c4e339d4a1d3fda0a9492017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-014i-2900000000-100cd0cc67ac9eda3f4e2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-014l-5900000000-79447b563349d08aacc02017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Indole ESI-ITFT , positive-QTOFsplash10-00kf-9800000000-a1ce5da5416e6d003ff92017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indole 10V, Positive-QTOFsplash10-014i-0900000000-aba5022e03d31dcbcc862016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indole 20V, Positive-QTOFsplash10-014i-0900000000-78c0f569df5b7f51c52c2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indole 40V, Positive-QTOFsplash10-014i-6900000000-bacb6e9a65a688229f962016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indole 10V, Negative-QTOFsplash10-014i-0900000000-e93b2f48040666dd7fe02016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indole 20V, Negative-QTOFsplash10-014i-0900000000-07d8a93ec0ace38ef3b32016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indole 40V, Negative-QTOFsplash10-014i-6900000000-8abfc9b162cc93f153ac2016-09-14Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Intestine
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected and Quantified32352.266 nmol/g wet fecesAdult (>18 years old)Not Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected and Quantified11962.0867 nmol/g wet fecesAdult (>18 years old)Not Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected and Quantified23400.619 nmol/g wet fecesAdult (>18 years old)Not Specified
Normal		 details
FecesDetected and Quantified300 +/- 6640 uMAdult (>18 years old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)Not Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)BothAutism details
FecesDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)BothPervasive Developmental Disorder Not Otherwise Specified details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Nonalcoholic fatty liver disease (NAFLD)		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn's disease 		details
FecesDetected and Quantified1684.0 +/- 84.4 uMNot SpecifiedNot SpecifiedClostridium difficile infection details
FecesDetected and Quantified762.8 +/- 53.8 uMNot SpecifiedNot Specifiednon-Clostridium difficile diarrhea details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Clostridium difficile infection 		details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Crohn's disease		 details
FecesDetected but not QuantifiedNot QuantifiedNot 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 QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>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 QuantifiedNot QuantifiedAdult (>18 years old)BothImmunoglobulin A nephropathy (IgAN) non progressor details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothImmunoglobulin A nephropathy (IgAN) progressor details
UrineDetected but not QuantifiedNot QuantifiedAdult (>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 ]
Clostridium difficile infection
  1. Darkoh C, Plants-Paris K, Bishoff D, DuPont HL: Clostridium difficile Modulates the Gut Microbiota by Inducing the Production of Indole, an Interkingdom Signaling and Antimicrobial Molecule. mSystems. 2019 Mar 19;4(2). pii: mSystems00346-18. doi: 10.1128/mSystems.00346-18. eCollection 2019 Mar-Apr. [PubMed:30944877 ]
  2. Patel M, Fowler D, Sizer J, Walton C: Faecal volatile biomarkers of Clostridium difficile infection. PLoS One. 2019 Apr 15;14(4):e0215256. doi: 10.1371/journal.pone.0215256. eCollection 2019. [PubMed:30986230 ]
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
FooDB 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 IDINDOLE
MarkerDB IDMDB00029881
Good Scents IDrw1006511
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. Raw I, Schmidt BJ, Merzel J: Catecholamines and congenital pain insensitivity. Braz J Med Biol Res. 1984;17(3-4):271-9. [PubMed:6085021 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. Scott AK: Sumatriptan clinical pharmacokinetics. Clin Pharmacokinet. 1994 Nov;27(5):337-44. [PubMed:7851052 ]
  7. 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 ]
  8. 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 ]
  9. 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 ]
  10. 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 ]
  11. Yoshida M, Mishiro Y: [Indole production in human whole saliva]. Shigaku. 1989 Aug;77(2):472-86. [PubMed:2489307 ]
  12. 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 ]
  13. 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 ]
  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 ]
  17. Patel M, Fowler D, Sizer J, Walton C: Faecal volatile biomarkers of Clostridium difficile infection. PLoS One. 2019 Apr 15;14(4):e0215256. doi: 10.1371/journal.pone.0215256. eCollection 2019. [PubMed:30986230 ]
  18. Kim J, Park W: Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration? J Microbiol. 2015 Jul;53(7):421-8. doi: 10.1007/s12275-015-5273-3. Epub 2015 Jun 27. [PubMed:26115989 ]
  19. Kumar A, Sperandio V: Indole Signaling at the Host-Microbiota-Pathogen Interface. mBio. 2019 Jun 4;10(3). pii: mBio.01031-19. doi: 10.1128/mBio.01031-19. [PubMed:31164470 ]

Enzymes

Enzyme Details
1. Aryl hydrocarbon receptor
General function:
Involved in transcription regulator activity
Specific function:
Ligand-activated transcriptional activator. Binds to the XRE promoter region of genes it activates. Activates the expression of multiple phase I and II xenobiotic chemical metabolizing enzyme genes (such as the CYP1A1 gene). Mediates biochemical and toxic effects of halogenated aromatic hydrocarbons. Involved in cell-cycle regulation. Likely to play an important role in the development and maturation of many tissues
Gene Name:
AHR
Uniprot ID:
P35869
Molecular weight:
96146.7