Showing metabocard for Indole (MMDBc0000004)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:37:37 UTC
Update Date2024-09-28 00:55:51 UTC
Metabolite IDMMDBc0000004
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9238008198>

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
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3D MOL for #<Metabolite:0x00007f9238008198>

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 #<Metabolite:0x00007f9238008198>

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>
MMDBc0000004

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007f9238008198>

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
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PDB for #<Metabolite:0x00007f9238008198>

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 #<Metabolite:0x00007f9238008198>

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 #<Metabolite:0x00007f9238008198>

N1C=CC2=C1C=CC=C2
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INCHI for #<Metabolite:0x00007f9238008198>

InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H
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Synonyms
ValueSource
2,3-BenzopyrroleChEBI
indolChEBI
1-AzaindeneHMDB
1-BenzazoleHMDB
Benzo[b]pyrroleHMDB
KetoleHMDB
IndoleHMDB
Molecular FormulaC8H7N
Average Mass117.1479
Monoisotopic Mass117.057849229
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