Showing metabocard for 3-Methylindole (MMDBc0000348)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:35:52 UTC
Update Date2024-04-30 19:31:53 UTC
Metabolite IDMMDBc0000348
Metabolite Identification
Common Name3-Methylindole
Description3-Methylindole, or skatole, belongs to the indole family and has a methyl substituent in position 3 of the indole ring. It occurs naturally in feces, beets, and coal tar, and has a strong fecal odor. Its name is derived from skato, the Greek word for dung. It exists as a white crystalline or fine powder solid, and it browns upon aging. 3-Methylindole is produced from tryptophan in the mammalian digestive tract where tryptophan is converted to indoleacetic acid, which decarboxylates to give the methylindole. These reactions are largely driven by the microbiota in the digestive tract. 3-Methylindole is soluble in alcohol and benzene and it gives violet color in potassium ferrocyanide (K4Fe(CN)6.3H2O) mixed with sulfuric acid (H2SO4). Skatole has a double ring system which displays aromaticity that comes from the lone pair electrons on the nitrogen. It is continuous (all atoms in the ring are sp2 hybridized), planar, and follows the 4n+2 rule because it has 10 pi electrons. In a 1994 report released by five top cigarette companies, skatole was listed as one of the 599 additives to cigarettes. This is because in low concentrations skatole has a flowery smell and is found in several flowers and essential oils, including those of orange blossoms, jasmine, and Ziziphus mauritiana. As a result, skatole/3-methylindole is used as a fragrance and fixative in many perfumes and as a general aroma compound for other applications. 3-Methylindole has been found to be a bacterial metabolite of members of the Clostridium (PMID: 18223109 ) and Lactobacillus (PMID: 16345702 ) families. Skatole functions as an insect attractant and is one of many compounds that are attractive to males of various species of orchid bees, which apparently gather the chemical to synthesize pheromones; it is commonly used as bait for these bees for study (PMID: 12647866 ). It is also known for being an attractant for the Tasmanian grass grub beetle (Aphodius tasmaniae). Skatole has also been shown to be an attractant to gravid mosquitoes in both field and laboratory conditions (PMID: 24242053 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fa4ecd72970>


  Mrv1652304272018132D          

 10 11  0  0  0  0            999 V2000
   -0.7930    2.1346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7182    0.9920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9645    1.3276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6320    0.1715    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  2  0  0  0  0
  6  7  2  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fa4ecd72970>

HMDB0000466
     RDKit          3D
3-Methylindole
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.5211   -0.7887    0.2015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3981    0.1812    0.0940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4564    1.5656    0.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1930    2.0173   -0.0474 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6505    0.9594   -0.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0357    0.8888   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6351   -0.3531   -0.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9306   -1.5365   -0.0748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5568   -1.4519    0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0691   -0.2191    0.0173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7563   -1.0454    1.2415 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3778   -1.6777   -0.4473 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4213   -0.2527   -0.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3843    2.1217    0.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0772    3.0225   -0.0985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6214    1.8123   -0.2309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7213   -0.3849   -0.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4159   -2.5156   -0.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0671   -2.3430    0.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
M  END
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3D SDF for #<Metabolite:0x00007fa4ecd72970>


  Mrv1652304272018132D          

 10 11  0  0  0  0            999 V2000
   -0.7930    2.1346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7182    0.9920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9645    1.3276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6320    0.1715    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  2  0  0  0  0
  6  7  2  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000348

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H9N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6,10H,1H3

> <INCHI_KEY>
ZFRKQXVRDFCRJG-UHFFFAOYSA-N

> <FORMULA>
C9H9N

> <MOLECULAR_WEIGHT>
131.1745

> <EXACT_MASS>
131.073499293

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.947043858415471

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methyl-1H-indole

> <ALOGPS_LOGP>
2.58

> <JCHEM_LOGP>
2.5854291983333333

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.483126674098358

> <JCHEM_POLAR_SURFACE_AREA>
15.79

> <JCHEM_REFRACTIVITY>
42.18569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.09e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
scatole

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x00007fa4ecd72970>

HMDB0000466
     RDKit          3D
3-Methylindole
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.5211   -0.7887    0.2015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3981    0.1812    0.0940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4564    1.5656    0.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1930    2.0173   -0.0474 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6505    0.9594   -0.0698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0357    0.8888   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6351   -0.3531   -0.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9306   -1.5365   -0.0748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5568   -1.4519    0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0691   -0.2191    0.0173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7563   -1.0454    1.2415 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3778   -1.6777   -0.4473 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4213   -0.2527   -0.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3843    2.1217    0.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0772    3.0225   -0.0985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6214    1.8123   -0.2309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7213   -0.3849   -0.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4159   -2.5156   -0.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0671   -2.3430    0.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
M  END
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PDB for #<Metabolite:0x00007fa4ecd72970>

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0      -1.480   3.985   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.207   1.852   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.800   2.478   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -3.046   0.320   0.000  0.00  0.00           N+0
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    8                                                       
CONECT    5    3    9                                                       
CONECT    6    7   10                                                       
CONECT    7    1    6    8                                                  
CONECT    8    4    7    9                                                  
CONECT    9    5    8   10                                                  
CONECT   10    6    9                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for #<Metabolite:0x00007fa4ecd72970>

COMPND    HMDB0000466
HETATM    1  C1  UNL     1       2.521  -0.789   0.202  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.398   0.181   0.094  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.456   1.566   0.053  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.193   2.017  -0.047  1.00  0.00           N  
HETATM    5  C4  UNL     1      -0.651   0.959  -0.070  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.036   0.889  -0.161  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.635  -0.353  -0.161  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.931  -1.536  -0.075  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.557  -1.452   0.015  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.069  -0.219   0.017  1.00  0.00           C  
HETATM   11  H1  UNL     1       2.756  -1.045   1.241  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.378  -1.678  -0.447  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.421  -0.253  -0.206  1.00  0.00           H  
HETATM   14  H4  UNL     1       2.384   2.122   0.097  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.077   3.023  -0.099  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.621   1.812  -0.231  1.00  0.00           H  
HETATM   17  H7  UNL     1      -3.721  -0.385  -0.233  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.416  -2.516  -0.076  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.067  -2.343   0.087  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    3   10
CONECT    3    4   14
CONECT    4    5   15
CONECT    5    6    6   10
CONECT    6    7   16
CONECT    7    8    8   17
CONECT    8    9   18
CONECT    9   10   10   19
END
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SMILES for #<Metabolite:0x00007fa4ecd72970>

CC1=CNC2=CC=CC=C12
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INCHI for #<Metabolite:0x00007fa4ecd72970>

InChI=1S/C9H9N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6,10H,1H3
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Synonyms
ValueSource
3-Methyl-4,5-benzopyrroleChEBI
beta-MethylindoleChEBI
SkatolChEBI
b-MethylindoleGenerator
Β-methylindoleGenerator
3-Methyl-1H-indoleHMDB
3-MIHMDB
ScatoleHMDB
SkatoleHMDB
3 MethylindoleHMDB
3-MethylindoleChEBI
Molecular FormulaC9H9N
Average Mass131.1745
Monoisotopic Mass131.073499293
IUPAC Name3-methyl-1H-indole
Traditional Namescatole
CAS Registry NumberNot Available
SMILES
CC1=CNC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H9N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6,10H,1H3
InChI KeyZFRKQXVRDFCRJG-UHFFFAOYSA-N