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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-01 14:38:06 UTC

Update Date

2021-09-26 22:48:59 UTC

HMDB ID

HMDB0242533

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Ibogamine

Description

Ibogamine belongs to the class of organic compounds known as ibogan-type alkaloids. These are indole alkaloids with a structure based on the ibogamine skeleton or a derivative thereof. Ibogamine is a pentacyclic heterocyclic compound consisting of an indole fused to an azepane-containing tricyclic moiety ring. Iboga alkaloids arise from the cyclization of a secodine-type precursor through the formation of a 16,21 bond. Ibogamine persistently reduced the self-administration of cocaine and morphine in rats. Ibogamine is a very strong basic compound (based on its pKa). Basic research related to how addiction affects the brain has used this chemical. While the related alkaloids Ibogaine(20-40 mg/kg), harmaline (10-40 mg/kg) and desethylcoronaridine (10-40 mg/kg) were "obviously tremorgenic". Ibogamine is an alkaloid found in Tabernanthe iboga. . The same study found that Ibogamine (40mg/kg) and Coronaridine (40mg/kg) did not produce "any tremor effects in rats that differ significantly from saline control". This compound has been identified in human blood as reported by (PMID: 31557052 ). Ibogamine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Ibogamine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0253329
     RDKit          3D
(1R,15R,17S,18S)-17-Ethyl-3,13-diazapentacyclo[13.3.1.02,10.04,9.013,18]nonad...
 45 49  0  0  0  0  0  0  0  0999 V2000
   -3.4777    1.0153    2.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6023   -0.2593    1.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858   -0.3954    0.1245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0729    0.6311   -0.9321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7349    0.9074   -1.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9085    1.6481   -0.5993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5976    0.7683    0.6022 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8606    0.4825    0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7831    1.4716    0.5626 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0209    0.9497    0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2881    1.4961    0.4866 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4161    0.6967    0.4132 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2873   -0.6832    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0269   -1.2215    0.3634 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9151   -0.4117    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5808   -0.6988    0.4640 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.7926   -0.9415   -2.6662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1784   -1.2593    1.2006 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1533004151519472D          

 21 25  0  0  0  0            999 V2000
   -1.5240    0.0343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7491    0.2094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0710   -0.5993    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6831   -1.1929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
HMDB0242533

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC1CC2CC3C1N(C2)CCC1=C3NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C19H24N2/c1-2-13-9-12-10-16-18-15(7-8-21(11-12)19(13)16)14-5-3-4-6-17(14)20-18/h3-6,12-13,16,19-20H,2,7-11H2,1H3

> <INCHI_KEY>
LRLCVRYKAFDXKU-UHFFFAOYSA-N

> <FORMULA>
C19H24N2

> <MOLECULAR_WEIGHT>
280.415

> <EXACT_MASS>
280.193948781

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
33.75999600485646

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
17-ethyl-3,13-diazapentacyclo[13.3.1.0²,¹⁰.0⁴,⁹.0¹³,¹⁸]nonadeca-2(10),4,6,8-tetraene

> <ALOGPS_LOGP>
4.24

> <JCHEM_LOGP>
3.6889304560000005

> <ALOGPS_LOGS>
-4.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.809121956413694

> <JCHEM_PKA_STRONGEST_BASIC>
9.065794542073654

> <JCHEM_POLAR_SURFACE_AREA>
19.03

> <JCHEM_REFRACTIVITY>
87.1093

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.54e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
17-ethyl-3,13-diazapentacyclo[13.3.1.0²,¹⁰.0⁴,⁹.0¹³,¹⁸]nonadeca-2(10),4,6,8-tetraene

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0253329
     RDKit          3D
(1R,15R,17S,18S)-17-Ethyl-3,13-diazapentacyclo[13.3.1.02,10.04,9.013,18]nonad...
 45 49  0  0  0  0  0  0  0  0999 V2000
   -3.4777    1.0153    2.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6023   -0.2593    1.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858   -0.3954    0.1245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0729    0.6311   -0.9321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7349    0.9074   -1.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9085    1.6481   -0.5993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5976    0.7683    0.6022 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8606    0.4825    0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7831    1.4716    0.5626 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0209    0.9497    0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2881    1.4961    0.4866 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.2873   -0.6832    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0269   -1.2215    0.3634 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9151   -0.4117    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5808   -0.6988    0.4640 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0190   -2.0715    0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7601   -1.0971   -0.8388 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0576   -0.4189   -2.0175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3006   -0.5646    0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4497    1.2676    2.6074 H   0  0  0  0  0  0  0  0  0  0  0  0
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 20 44  1  0
 21 45  1  0
M  END

HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         0                                  
HETATM    1  C   UNK     0      -2.845   0.064   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.409  -0.492   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.209   0.474   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.045   2.013   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.622   1.838   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.733   2.933   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.947   1.384   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.398   0.391   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       1.999  -1.119   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.142  -2.227   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.666  -1.771   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.370  -0.352   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.572   0.964   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       5.577   2.131   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       6.997   1.535   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.390   2.191   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.655   1.313   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.527  -0.222   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.134  -0.878   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.869   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.483   0.342   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8   10   21                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   20                                                  
CONECT   13   12    7   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   12   15                                                  
CONECT   21    9    5                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   50    0
END

COMPND    HMDB0242533
HETATM    1  C1  UNL     1      -3.171   0.607   2.326  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.767   0.242   0.960  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.743  -0.578   0.258  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.143  -1.044  -1.122  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.045  -0.491  -2.049  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.779  -1.251  -1.659  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.369  -0.931  -0.247  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.022  -0.610   0.010  1.00  0.00           C  
HETATM    9  N1  UNL     1       1.893  -1.569   0.451  1.00  0.00           N  
HETATM   10  C9  UNL     1       3.111  -1.073   0.632  1.00  0.00           C  
HETATM   11  C10 UNL     1       4.325  -1.579   1.052  1.00  0.00           C  
HETATM   12  C11 UNL     1       5.452  -0.786   1.141  1.00  0.00           C  
HETATM   13  C12 UNL     1       5.391   0.569   0.803  1.00  0.00           C  
HETATM   14  C13 UNL     1       4.217   1.094   0.389  1.00  0.00           C  
HETATM   15  C14 UNL     1       3.095   0.262   0.311  1.00  0.00           C  
HETATM   16  C15 UNL     1       1.832   0.519  -0.061  1.00  0.00           C  
HETATM   17  C16 UNL     1       1.345   1.871  -0.512  1.00  0.00           C  
HETATM   18  C17 UNL     1      -0.112   1.849  -0.562  1.00  0.00           C  
HETATM   19  N2  UNL     1      -1.358   1.331  -0.528  1.00  0.00           N  
HETATM   20  C18 UNL     1      -2.031   0.975  -1.793  1.00  0.00           C  
HETATM   21  C19 UNL     1      -1.408   0.056   0.234  1.00  0.00           C  
HETATM   22  H1  UNL     1      -3.976   0.873   3.040  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.521   1.486   2.203  1.00  0.00           H  
HETATM   24  H3  UNL     1      -2.544  -0.240   2.666  1.00  0.00           H  
HETATM   25  H4  UNL     1      -4.718  -0.293   1.098  1.00  0.00           H  
HETATM   26  H5  UNL     1      -3.952   1.204   0.443  1.00  0.00           H  
HETATM   27  H6  UNL     1      -2.614  -1.524   0.855  1.00  0.00           H  
HETATM   28  H7  UNL     1      -3.236  -2.124  -1.224  1.00  0.00           H  
HETATM   29  H8  UNL     1      -4.068  -0.496  -1.418  1.00  0.00           H  
HETATM   30  H9  UNL     1      -2.261  -0.676  -3.099  1.00  0.00           H  
HETATM   31  H10 UNL     1      -1.079  -2.336  -1.789  1.00  0.00           H  
HETATM   32  H11 UNL     1       0.033  -1.127  -2.408  1.00  0.00           H  
HETATM   33  H12 UNL     1      -0.640  -1.859   0.353  1.00  0.00           H  
HETATM   34  H13 UNL     1       1.654  -2.583   0.634  1.00  0.00           H  
HETATM   35  H14 UNL     1       4.426  -2.615   1.323  1.00  0.00           H  
HETATM   36  H15 UNL     1       6.412  -1.152   1.464  1.00  0.00           H  
HETATM   37  H16 UNL     1       6.269   1.185   0.873  1.00  0.00           H  
HETATM   38  H17 UNL     1       4.093   2.125   0.115  1.00  0.00           H  
HETATM   39  H18 UNL     1       1.839   2.166  -1.494  1.00  0.00           H  
HETATM   40  H19 UNL     1       1.749   2.696   0.132  1.00  0.00           H  
HETATM   41  H20 UNL     1       0.075   0.958  -1.254  1.00  0.00           H  
HETATM   42  H21 UNL     1      -0.087   1.712   0.572  1.00  0.00           H  
HETATM   43  H22 UNL     1      -3.057   1.347  -1.766  1.00  0.00           H  
HETATM   44  H23 UNL     1      -1.447   1.460  -2.625  1.00  0.00           H  
HETATM   45  H24 UNL     1      -1.107   0.348   1.273  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25   26
CONECT    3    4   21   27
CONECT    4    5   28   29
CONECT    5    6   20   30
CONECT    6    7   31   32
CONECT    7    8   21   33
CONECT    8    9   16   16
CONECT    9   10   34
CONECT   10   11   11   15
CONECT   11   12   35
CONECT   12   13   13   36
CONECT   13   14   37
CONECT   14   15   15   38
CONECT   15   16
CONECT   16   17
CONECT   17   18   39   40
CONECT   18   19   41   42
CONECT   19   20   21
CONECT   20   43   44
CONECT   21   45
END

HMDB0253329
     RDKit          3D
(1R,15R,17S,18S)-17-Ethyl-3,13-diazapentacyclo[13.3.1.02,10.04,9.013,18]nonad...
 45 49  0  0  0  0  0  0  0  0999 V2000
   -3.4777    1.0153    2.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6023   -0.2593    1.3596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858   -0.3954    0.1245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0729    0.6311   -0.9321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7349    0.9074   -1.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9085    1.6481   -0.5993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5976    0.7683    0.6022 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8606    0.4825    0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7831    1.4716    0.5626 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0209    0.9497    0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2881    1.4961    0.4866 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4161    0.6967    0.4132 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2873   -0.6832    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0269   -1.2215    0.3634 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9151   -0.4117    0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5808   -0.6988    0.4640 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0190   -2.0715    0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0798   -2.1806   -0.7944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7601   -1.0971   -0.8388 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0576   -0.4189   -2.0175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3006   -0.5646    0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4497    1.2676    2.6074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1332    1.8802    1.5144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7568    0.8777    2.9341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3252   -1.1305    2.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6738   -0.4273    1.1225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1003   -1.3831   -0.3384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8402    0.2898   -1.6647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4099    1.5965   -0.5421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8568    1.5680   -2.4945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0147    2.0796   -1.0474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5676    2.4629   -0.2118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8284    1.2288    1.5565 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6126    2.5085    0.6179 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4442    2.5813    0.5342 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4189    1.1306    0.4033 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1284   -1.3575    0.2921 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9257   -2.2959    0.3146 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5309   -2.3672    1.3460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8395   -2.7966    0.2227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4930   -3.1301   -0.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6784   -2.2807   -1.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1671   -0.1659   -2.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7926   -0.9415   -2.6662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1784   -1.2593    1.2006 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  1  0
 21  3  1  0
 20  5  1  0
 21  7  1  0
 16  8  2  0
 15 10  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  9 34  1  0
 11 35  1  0
 12 36  1  0
 13 37  1  0
 14 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 20 43  1  0
 20 44  1  0
 21 45  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₉H₂₄N₂

Average Molecular Weight

280.415

Monoisotopic Molecular Weight

280.193948781

IUPAC Name

17-ethyl-3,13-diazapentacyclo[13.3.1.0²,¹⁰.0⁴,⁹.0¹³,¹⁸]nonadeca-2(10),4,6,8-tetraene

Traditional Name

17-ethyl-3,13-diazapentacyclo[13.3.1.0²,¹⁰.0⁴,⁹.0¹³,¹⁸]nonadeca-2(10),4,6,8-tetraene

CAS Registry Number

Not Available

SMILES

CCC1CC2CC3C1N(C2)CCC1=C3NC2=CC=CC=C12

InChI Identifier

InChI=1S/C19H24N2/c1-2-13-9-12-10-16-18-15(7-8-21(11-12)19(13)16)14-5-3-4-6-17(14)20-18/h3-6,12-13,16,19-20H,2,7-11H2,1H3

InChI Key

LRLCVRYKAFDXKU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ibogan-type alkaloids. These are indole alkaloids with a structure based on the ibogamine skeleton or a derivative thereof. Ibogamine is a pentacyclic heterocyclic compound consisting of an indole fused to an azepane-containing tricyclic moiety ring. Iboga alkaloids arise from the cyclization of a secodine-type precursor through the formation of a 16,21 bond.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Ibogan-type alkaloids

Sub Class

Not Available

Direct Parent

Ibogan-type alkaloids

Alternative Parents

Substituents

Ibogan skeleton
Catharanthine skeleton
Pyrroloazepine
3-alkylindole
Indole
Indole or derivatives
Azepine
Aralkylamine
Piperidine
Benzenoid
Pyrrole
Heteroaromatic compound
Tertiary aliphatic amine
Tertiary amine
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	4.24	ALOGPS
logP	3.69	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	16.81	ChemAxon
pKa (Strongest Basic)	9.07	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	19.03 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	87.11 m³·mol⁻¹	ChemAxon
Polarizability	33.76 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	198.912	30932474
DeepCCS	[M+Na]+	174.477	30932474
AllCCS	[M+H]+	170.2	32859911
AllCCS	[M+H-H2O]+	166.7	32859911
AllCCS	[M+NH4]+	173.4	32859911
AllCCS	[M+Na]+	174.3	32859911
AllCCS	[M-H]-	180.7	32859911
AllCCS	[M+Na-2H]-	180.3	32859911
AllCCS	[M+HCOO]-	180.0	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ibogamine,1TMS,isomer #1	CCC1CC2CC3C4=C(CCN(C2)C13)C1=CC=CC=C1N4[Si](C)(C)C	2662.2	Semi standard non polar	33892256
Ibogamine,1TMS,isomer #1	CCC1CC2CC3C4=C(CCN(C2)C13)C1=CC=CC=C1N4[Si](C)(C)C	2548.1	Standard non polar	33892256
Ibogamine,1TMS,isomer #1	CCC1CC2CC3C4=C(CCN(C2)C13)C1=CC=CC=C1N4[Si](C)(C)C	3192.7	Standard polar	33892256
Ibogamine,1TBDMS,isomer #1	CCC1CC2CC3C4=C(CCN(C2)C13)C1=CC=CC=C1N4[Si](C)(C)C(C)(C)C	2846.2	Semi standard non polar	33892256
Ibogamine,1TBDMS,isomer #1	CCC1CC2CC3C4=C(CCN(C2)C13)C1=CC=CC=C1N4[Si](C)(C)C(C)(C)C	2827.6	Standard non polar	33892256
Ibogamine,1TBDMS,isomer #1	CCC1CC2CC3C4=C(CCN(C2)C13)C1=CC=CC=C1N4[Si](C)(C)C(C)(C)C	3303.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Ibogamine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udi-3090000000-8e971cbbf8157db93708	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ibogamine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ibogamine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ibogamine 10V, Negative-QTOF	splash10-004i-0090000000-fa0545de4a4dc60fd062	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ibogamine 20V, Negative-QTOF	splash10-004i-0090000000-fa0545de4a4dc60fd062	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ibogamine 40V, Negative-QTOF	splash10-0h01-0190000000-00bcae744c72c6a480c8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ibogamine 10V, Positive-QTOF	splash10-001i-0090000000-633af5025278f639cee6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ibogamine 20V, Positive-QTOF	splash10-001i-0090000000-633af5025278f639cee6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ibogamine 40V, Positive-QTOF	splash10-0w2c-0890000000-2a149e83f9b2778d3524	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ibogamine

METLIN ID

Not Available

PubChem Compound

500053

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Ibogamine (HMDB0242533)

MOL for HMDB0242533 (Ibogamine)

3D MOL for HMDB0242533 (Ibogamine)

3D SDF for HMDB0242533 (Ibogamine)

3D-SDF for HMDB0242533 (Ibogamine)

PDB for HMDB0242533 (Ibogamine)

3D PDB for HMDB0242533 (Ibogamine)

SMILES for HMDB0242533 (Ibogamine)

INCHI for HMDB0242533 (Ibogamine)

Structure for HMDB0242533 (Ibogamine)

3D Structure for HMDB0242533 (Ibogamine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra