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Showing NP-Card for 3-Methylindole (NP0000802)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:39:37 UTC
NP-MRD IDNP0000802
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000802 (3-Methylindole)


  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
Download

3D MOL for NP0000802 (3-Methylindole)

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
Download

3D SDF for NP0000802 (3-Methylindole)


  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>
NP0000802

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000802 (3-Methylindole)

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 NP0000802 (3-Methylindole)

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 NP0000802 (3-Methylindole)

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 NP0000802 (3-Methylindole)

CC1=CNC2=CC=CC=C12
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INCHI for NP0000802 (3-Methylindole)

InChI=1S/C9H9N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6,10H,1H3
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View in JSmol
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
Chemical FormulaC9H9N
Average Mass131.1745 Da
Monoisotopic Mass131.07350 Da
IUPAC Name3-methyl-1H-indole
Traditional Namescatole
CAS Registry Number83-34-1
SMILES
CC1=CNC2=C1C=CC=C2
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arum spp.KNApSAcK Database
Beta vulgarisKNApSAcK Database
Cephalonomia gallicolaLOTUS Database
Coprinopsis picaceaLOTUS Database
Giraffa camelopardalisLOTUS Database
Nectandra spp.KNApSAcK Database
Salvia divinorumLOTUS Database
Sauromatum venosumLOTUS Database
Tachigali myrmecophilaLOTUS Database
Tecoma stansLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-methylindoles. These are aromatic heterocyclic compounds that contain an indole moiety substituted at the 3-position with a methyl group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassIndoles
Direct Parent3-methylindoles
Alternative Parents
Substituents
  • 3-methylindole
  • Benzenoid
  • Substituted pyrrole
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point97.5 °CNot Available
Boiling Point265.00 to 266.00 °C. @ 755.00 mm HgThe Good Scents Company Information System
Water Solubility0.5 mg/mLNot Available
LogP2.60Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility3.09 g/LALOGPS
logP2.58ALOGPS
logP2.59ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)17.48ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area15.79 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.19 m³·mol⁻¹ChemAxon
Polarizability14.95 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000466
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB004302
KNApSAcK IDC00001430
Chemspider ID6480
KEGG Compound IDC08313
BioCyc IDSKATOLE
BiGG IDNot Available
Wikipedia LinkSkatole
METLIN ID5453
PubChem Compound6736
PDB IDNot Available
ChEBI ID9171
Good Scents IDrw1006331
References
General References
  1. Karlin DA, Mastromarino AJ, Jones RD, Stroehlein JR, Lorentz O: Fecal skatole and indole and breath methane and hydrogen in patients with large bowel polyps or cancer. J Cancer Res Clin Oncol. 1985;109(2):135-41. [PubMed:3980562 ]
  2. Moore JG, Jessop LD, Osborne DN: Gas-chromatographic and mass-spectrometric analysis of the odor of human feces. Gastroenterology. 1987 Dec;93(6):1321-9. [PubMed:3678751 ]
  3. 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 ]
  4. Zuccato E, Venturi M, Di Leo G, Colombo L, Bertolo C, Doldi SB, Mussini E: Role of bile acids and metabolic activity of colonic bacteria in increased risk of colon cancer after cholecystectomy. Dig Dis Sci. 1993 Mar;38(3):514-9. [PubMed:8444084 ]
  5. Codipilly DP, Kaufman HW, Kleinberg I: Use of a novel group of oral malodor measurements to evaluate an anti-oral malodor mouthrinse (TriOralTM) in humans. J Clin Dent. 2004;15(4):98-104. [PubMed:15794454 ]
  6. Whitehead TR, Price NP, Drake HL, Cotta MA: Catabolic pathway for the production of skatole and indoleacetic acid by the acetogen Clostridium drakei, Clostridium scatologenes, and swine manure. Appl Environ Microbiol. 2008 Mar;74(6):1950-3. doi: 10.1128/AEM.02458-07. Epub 2008 Jan 25. [PubMed:18223109 ]
  7. Yokoyama MT, Carlson JR: Production of Skatole and para-Cresol by a Rumen Lactobacillus sp. Appl Environ Microbiol. 1981 Jan;41(1):71-6. doi: 10.1128/aem.41.1.71-76.1981. [PubMed:16345702 ]
  8. Beehler JW, Millar JG, Mulla MS: Field evaluation of synthetic compounds mediating oviposition inCulex mosquitoes (Diptera: Culicidae). J Chem Ecol. 1994 Feb;20(2):281-91. doi: 10.1007/BF02064436. [PubMed:24242053 ]