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Showing metabocard for 3-Methylene-indolenine (HMDB0011664)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-02-03 11:51:29 UTC
Update Date2023-02-21 17:17:33 UTC
HMDB IDHMDB0011664
Secondary Accession Numbers
  • HMDB11664
Metabolite Identification
Common Name3-Methylene-indolenine
Description3-Methylene-indolenine is an electrophilic molecule produced by the action of cytochrome P450 2F1 on 3-methylindole (3MI). 3-Methylindole (3MI) is a naturally occurring pulmonary toxin that requires metabolic activation. In particular, 3MI-induced pneumotoxicity arises from cytochrome P-450-catalyzed dehydrogenation of 3MI to an electrophilic methylene imine (3-methyleneindolenine), which covalently binds to cellular macromolecules. Members of the CYP2F gene subfamily are selectively expressed in lung tissues and have been implicated as important catalysts in the formation of reactive intermediates from several pneumotoxic chemicals. (PMID: 10383923 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011664 (3-Methylene-indolenine)

  Mrv0541 02241201492D          

 10 11  0  0  0  0            999 V2000
    9.3522   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3522   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -5.6060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -7.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1367   -5.7637    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6215   -6.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1366   -7.0985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3914   -7.8832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  1  1  0  0  0  0
  2  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
  9  2  1  0  0  0  0
 10  9  2  0  0  0  0
M  END
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3D MOL for HMDB0011664 (3-Methylene-indolenine)

HMDB0011664
     RDKit          3D
3-Methylene-indolenine
 17 18  0  0  0  0  0  0  0  0999 V2000
    2.3997   -1.2705   -0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6241   -0.2058   -0.2551 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0142    1.1995   -0.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.9272    0.0065 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2109    1.1550    0.1207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5396    1.4804    0.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4658    0.4700    0.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0988   -0.8711    0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7747   -1.1798    0.0224 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1843   -0.1704   -0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9847   -2.2463   -0.4666 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4647   -1.1740   -0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0387    1.5752   -0.3250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8361    2.5047    0.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5200    0.6511    0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8258   -1.6575    0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4116   -2.1878   -0.1093 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  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
  3 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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3D SDF for HMDB0011664 (3-Methylene-indolenine)

  Mrv0541 02241201492D          

 10 11  0  0  0  0            999 V2000
    9.3522   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3522   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -5.6060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -7.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1367   -5.7637    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6215   -6.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1366   -7.0985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3914   -7.8832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  1  1  0  0  0  0
  2  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
  9  2  1  0  0  0  0
 10  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011664

> <DATABASE_NAME>
hmdb

> <SMILES>
C=C1C=NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H7N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6H,1H2

> <INCHI_KEY>
BCNUXXXHEIUHJB-UHFFFAOYSA-N

> <FORMULA>
C9H7N

> <MOLECULAR_WEIGHT>
129.1586

> <EXACT_MASS>
129.057849229

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
14.083628644599568

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylidene-3H-indole

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
2.2309315876666664

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.306820778042735

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
43.505700000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.36e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyleneindolenine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0011664 (3-Methylene-indolenine)

HMDB0011664
     RDKit          3D
3-Methylene-indolenine
 17 18  0  0  0  0  0  0  0  0999 V2000
    2.3997   -1.2705   -0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6241   -0.2058   -0.2551 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0142    1.1995   -0.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.9272    0.0065 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2109    1.1550    0.1207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5396    1.4804    0.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4658    0.4700    0.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0988   -0.8711    0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7747   -1.1798    0.0224 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1843   -0.1704   -0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9847   -2.2463   -0.4666 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4647   -1.1740   -0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0387    1.5752   -0.3250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8361    2.5047    0.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5200    0.6511    0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8258   -1.6575    0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4116   -2.1878   -0.1093 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  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
  3 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0011664 (3-Methylene-indolenine)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      17.457 -11.235   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.457 -12.775   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.124 -10.465   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.124 -13.545   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.790 -11.235   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.790 -12.775   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      18.922 -10.759   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      19.827 -12.005   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.922 -13.251   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.397 -14.715   0.000  0.00  0.00           C+0
CONECT    1    3    7    2                                                  
CONECT    2    4    1    9                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5                                                       
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0011664 (3-Methylene-indolenine)

COMPND    HMDB0011664
HETATM    1  C1  UNL     1       2.400  -1.271  -0.452  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.624  -0.206  -0.255  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.014   1.199  -0.203  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.973   1.927   0.006  1.00  0.00           N  
HETATM    5  C4  UNL     1      -0.211   1.155   0.121  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.540   1.480   0.342  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.466   0.470   0.400  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.099  -0.871   0.241  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.775  -1.180   0.022  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.184  -0.170  -0.040  1.00  0.00           C  
HETATM   11  H1  UNL     1       1.985  -2.246  -0.467  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.465  -1.174  -0.601  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.039   1.575  -0.325  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.836   2.505   0.465  1.00  0.00           H  
HETATM   15  H5  UNL     1      -3.520   0.651   0.569  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.826  -1.658   0.287  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.412  -2.188  -0.109  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   10
CONECT    3    4    4   13
CONECT    4    5
CONECT    5    6    6   10
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10   17
END
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SMILES for HMDB0011664 (3-Methylene-indolenine)

C=C1C=NC2=CC=CC=C12
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INCHI for HMDB0011664 (3-Methylene-indolenine)

InChI=1S/C9H7N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6H,1H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Methylene-3H-indoleHMDB
3-MethyleneindolenineHMDB
3-Methyleneindolenine, conjugate acidMeSH, HMDB
3-Methylene-indolenineMeSH
Chemical FormulaC9H7N
Average Molecular Weight129.1586
Monoisotopic Molecular Weight129.057849229
IUPAC Name3-methylidene-3H-indole
Traditional Name3-methyleneindolenine
CAS Registry Number40642-83-9
SMILES
C=C1C=NC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H7N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6H,1H2
InChI KeyBCNUXXXHEIUHJB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassNot Available
Direct ParentIndoles and derivatives
Alternative Parents
Substituents
  • Indole or derivatives
  • Benzenoid
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Imine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028355
KNApSAcK IDNot Available
Chemspider ID148991
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound170404
PDB IDNot Available
ChEBI ID63905
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Lanza DL, Code E, Crespi CL, Gonzalez FJ, Yost GS: Specific dehydrogenation of 3-methylindole and epoxidation of naphthalene by recombinant human CYP2F1 expressed in lymphoblastoid cells. Drug Metab Dispos. 1999 Jul;27(7):798-803. [PubMed:10383923 ]