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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 20:21:52 UTC

Update Date

2021-09-26 23:15:47 UTC

HMDB ID

HMDB0258676

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline

Description

1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline, also known as 1-TCMTC, belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole. Based on a literature review a significant number of articles have been published on 1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-trichloromethyl-1,2,3,4-tetrahydro-beta-carboline is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline 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

HMDB0258676
     RDKit          3D
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline
 28 30  0  0  0  0  0  0  0  0999 V2000
   -2.1107   -3.1374   -0.8648 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.7501   -1.8285    0.1704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6306   -2.2384    1.8794 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4848   -1.6179   -0.2509 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0599   -0.5615   -0.1509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5252    0.5380    0.6461 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9730    1.7982    0.2993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8305    1.7208   -0.6919 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0760    0.5796   -0.3224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877   -0.6194   -0.0393 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3635   -1.4895    0.2594 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5899   -0.9222    0.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8722   -1.3605    0.3876 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9496   -0.4969    0.2228 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7709    0.8312   -0.1503 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4787    1.2701   -0.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4178    0.3962   -0.1851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2868   -0.2999   -1.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5646    0.5205    0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5862    2.3231    1.1946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770    2.4405   -0.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2280    2.6296   -0.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1805    1.5062   -1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1680   -2.4919    0.5194 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0194   -2.3887    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9557   -0.8758    0.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6067    1.4765   -0.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3073    2.2979   -0.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 10  5  1  0
 17 12  1  0
 17  9  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
 11 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
M  END


  Mrv1652309112122222D          

 17 19  0  0  0  0            999 V2000
    2.8985   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.5840    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339    1.5105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6633    1.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9182    2.7664    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.4479    1.7268    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.8787    2.2367    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  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
  1  6  1  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
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258676

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC(Cl)(Cl)C1NCCC2=C1NC1=CC=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C12H11Cl3N2/c13-12(14,15)11-10-8(5-6-16-11)7-3-1-2-4-9(7)17-10/h1-4,11,16-17H,5-6H2

> <INCHI_KEY>
DPPAKKMPHBZNQA-UHFFFAOYSA-N

> <FORMULA>
C12H11Cl3N2

> <MOLECULAR_WEIGHT>
289.58

> <EXACT_MASS>
287.9987815

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
27.750972550181054

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(trichloromethyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indole

> <ALOGPS_LOGP>
3.24

> <JCHEM_LOGP>
3.2251693626666667

> <ALOGPS_LOGS>
-4.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.289844849159675

> <JCHEM_PKA_STRONGEST_BASIC>
5.84096052095832

> <JCHEM_POLAR_SURFACE_AREA>
27.82

> <JCHEM_REFRACTIVITY>
73.20429999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.65e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(trichloromethyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indole

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0258676
     RDKit          3D
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline
 28 30  0  0  0  0  0  0  0  0999 V2000
   -2.1107   -3.1374   -0.8648 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.7501   -1.8285    0.1704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6306   -2.2384    1.8794 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4848   -1.6179   -0.2509 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0599   -0.5615   -0.1509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5252    0.5380    0.6461 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9730    1.7982    0.2993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8305    1.7208   -0.6919 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0760    0.5796   -0.3224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877   -0.6194   -0.0393 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3635   -1.4895    0.2594 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5899   -0.9222    0.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8722   -1.3605    0.3876 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9496   -0.4969    0.2228 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7709    0.8312   -0.1503 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4787    1.2701   -0.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4178    0.3962   -0.1851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2868   -0.2999   -1.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5646    0.5205    0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5862    2.3231    1.1946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770    2.4405   -0.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2280    2.6296   -0.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1805    1.5062   -1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1680   -2.4919    0.5194 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0194   -2.3887    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9557   -0.8758    0.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6067    1.4765   -0.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3073    2.2979   -0.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 10  5  1  0
 17 12  1  0
 17  9  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
 11 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       5.410  -0.695   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.917  -0.374   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.393   1.090   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.362   2.235   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.856   1.914   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.380   0.450   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.840   0.450   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.810  -0.695   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.303  -0.374   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.173   1.090   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.858   2.235   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.364   1.914   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       3.610   2.820   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       6.838   3.699   0.000  0.00  0.00           C+0
HETATM   15 Cl   UNK     0       7.314   5.164   0.000  0.00  0.00          Cl+0
HETATM   16 Cl   UNK     0       8.303   3.223   0.000  0.00  0.00          Cl+0
HETATM   17 Cl   UNK     0       5.374   4.175   0.000  0.00  0.00          Cl+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   14                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7   13                                                  
CONECT   13   12    5                                                       
CONECT   14    4   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0258676
HETATM    1 CL1  UNL     1      -2.111  -3.137  -0.865  1.00  0.00          CL  
HETATM    2  C1  UNL     1      -2.750  -1.828   0.170  1.00  0.00           C  
HETATM    3 CL2  UNL     1      -2.631  -2.238   1.879  1.00  0.00          CL  
HETATM    4 CL3  UNL     1      -4.485  -1.618  -0.251  1.00  0.00          CL  
HETATM    5  C2  UNL     1      -2.060  -0.561  -0.151  1.00  0.00           C  
HETATM    6  N1  UNL     1      -2.525   0.538   0.646  1.00  0.00           N  
HETATM    7  C3  UNL     1      -1.973   1.798   0.299  1.00  0.00           C  
HETATM    8  C4  UNL     1      -0.830   1.721  -0.692  1.00  0.00           C  
HETATM    9  C5  UNL     1       0.076   0.580  -0.322  1.00  0.00           C  
HETATM   10  C6  UNL     1      -0.588  -0.619  -0.039  1.00  0.00           C  
HETATM   11  N2  UNL     1       0.363  -1.490   0.259  1.00  0.00           N  
HETATM   12  C7  UNL     1       1.590  -0.922   0.185  1.00  0.00           C  
HETATM   13  C8  UNL     1       2.872  -1.361   0.388  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.950  -0.497   0.223  1.00  0.00           C  
HETATM   15  C10 UNL     1       3.771   0.831  -0.150  1.00  0.00           C  
HETATM   16  C11 UNL     1       2.479   1.270  -0.354  1.00  0.00           C  
HETATM   17  C12 UNL     1       1.418   0.396  -0.185  1.00  0.00           C  
HETATM   18  H1  UNL     1      -2.287  -0.300  -1.222  1.00  0.00           H  
HETATM   19  H2  UNL     1      -3.565   0.521   0.749  1.00  0.00           H  
HETATM   20  H3  UNL     1      -1.586   2.323   1.195  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.777   2.441  -0.112  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.228   2.630  -0.608  1.00  0.00           H  
HETATM   23  H6  UNL     1      -1.180   1.506  -1.714  1.00  0.00           H  
HETATM   24  H7  UNL     1       0.168  -2.492   0.519  1.00  0.00           H  
HETATM   25  H8  UNL     1       3.019  -2.389   0.677  1.00  0.00           H  
HETATM   26  H9  UNL     1       4.956  -0.876   0.391  1.00  0.00           H  
HETATM   27  H10 UNL     1       4.607   1.476  -0.271  1.00  0.00           H  
HETATM   28  H11 UNL     1       2.307   2.298  -0.645  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    4    5
CONECT    5    6   10   18
CONECT    6    7   19
CONECT    7    8   20   21
CONECT    8    9   22   23
CONECT    9   10   10   17
CONECT   10   11
CONECT   11   12   24
CONECT   12   13   13   17
CONECT   13   14   25
CONECT   14   15   15   26
CONECT   15   16   27
CONECT   16   17   17   28
END

HMDB0258676
     RDKit          3D
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline
 28 30  0  0  0  0  0  0  0  0999 V2000
   -2.1107   -3.1374   -0.8648 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.7501   -1.8285    0.1704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6306   -2.2384    1.8794 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4848   -1.6179   -0.2509 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0599   -0.5615   -0.1509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5252    0.5380    0.6461 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9730    1.7982    0.2993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8305    1.7208   -0.6919 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0760    0.5796   -0.3224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877   -0.6194   -0.0393 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3635   -1.4895    0.2594 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5899   -0.9222    0.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8722   -1.3605    0.3876 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9496   -0.4969    0.2228 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7709    0.8312   -0.1503 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4787    1.2701   -0.3539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4178    0.3962   -0.1851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2868   -0.2999   -1.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5646    0.5205    0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5862    2.3231    1.1946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770    2.4405   -0.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2280    2.6296   -0.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1805    1.5062   -1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1680   -2.4919    0.5194 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0194   -2.3887    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9557   -0.8758    0.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6067    1.4765   -0.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3073    2.2979   -0.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 10  5  1  0
 17 12  1  0
 17  9  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
 11 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Trichloromethyl-1,2,3,4-tetrahydro-b-carboline	Generator
1-Trichloromethyl-1,2,3,4-tetrahydro-β-carboline	Generator
1-TCMTC	HMDB

Chemical Formula

C₁₂H₁₁Cl₃N₂

Average Molecular Weight

289.58

Monoisotopic Molecular Weight

287.9987815

IUPAC Name

1-(trichloromethyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indole

Traditional Name

1-(trichloromethyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indole

CAS Registry Number

Not Available

SMILES

ClC(Cl)(Cl)C1NCCC2=C1NC1=CC=CC=C21

InChI Identifier

InChI=1S/C12H11Cl3N2/c13-12(14,15)11-10-8(5-6-16-11)7-3-1-2-4-9(7)17-10/h1-4,11,16-17H,5-6H2

InChI Key

DPPAKKMPHBZNQA-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Harmala alkaloids

Sub Class

Not Available

Direct Parent

Harmala alkaloids

Alternative Parents

Substituents

Harman
Beta-carboline
Pyridoindole
3-alkylindole
Indole
Indole or derivatives
Aralkylamine
Benzenoid
Heteroaromatic compound
Pyrrole
Secondary aliphatic amine
Azacycle
Organoheterocyclic compound
Secondary amine
Organohalogen compound
Amine
Hydrocarbon derivative
Organic nitrogen compound
Organopnictogen compound
Alkyl chloride
Organochloride
Organonitrogen compound
Alkyl halide
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)

Source

Exogenous

Exogenous (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	3.24	ALOGPS
logP	3.23	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	16.29	ChemAxon
pKa (Strongest Basic)	5.84	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	27.82 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	73.2 m³·mol⁻¹	ChemAxon
Polarizability	27.75 Å³	ChemAxon
Number of Rings	3	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]-	178.921	30932474
DeepCCS	[M+Na]+	153.578	30932474
AllCCS	[M+H]+	158.3	32859911
AllCCS	[M+H-H2O]+	154.7	32859911
AllCCS	[M+NH4]+	161.6	32859911
AllCCS	[M+Na]+	162.5	32859911
AllCCS	[M-H]-	156.9	32859911
AllCCS	[M+Na-2H]-	156.6	32859911
AllCCS	[M+HCOO]-	156.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	4.7 minutes	32390414
Predicted by Siyang on May 30, 2022	11.1027 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.02 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1493.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	337.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	131.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	210.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	200.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	390.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	374.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	254.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	823.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	384.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1170.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	305.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	293.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	380.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	149.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	11.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline	ClC(Cl)(Cl)C1NCCC2=C1NC1=CC=CC=C21	3144.1	Standard polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline	ClC(Cl)(Cl)C1NCCC2=C1NC1=CC=CC=C21	1979.9	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline	ClC(Cl)(Cl)C1NCCC2=C1NC1=CC=CC=C21	2416.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TMS,isomer #1	C[Si](C)(C)N1CCC2=C([NH]C3=CC=CC=C23)C1C(Cl)(Cl)Cl	2349.3	Semi standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TMS,isomer #1	C[Si](C)(C)N1CCC2=C([NH]C3=CC=CC=C23)C1C(Cl)(Cl)Cl	2386.4	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TMS,isomer #1	C[Si](C)(C)N1CCC2=C([NH]C3=CC=CC=C23)C1C(Cl)(Cl)Cl	2800.9	Standard polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TMS,isomer #2	C[Si](C)(C)N1C2=C(CCNC2C(Cl)(Cl)Cl)C2=CC=CC=C21	2409.3	Semi standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TMS,isomer #2	C[Si](C)(C)N1C2=C(CCNC2C(Cl)(Cl)Cl)C2=CC=CC=C21	2337.2	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TMS,isomer #2	C[Si](C)(C)N1C2=C(CCNC2C(Cl)(Cl)Cl)C2=CC=CC=C21	2874.1	Standard polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,2TMS,isomer #1	C[Si](C)(C)N1CCC2=C(C1C(Cl)(Cl)Cl)N([Si](C)(C)C)C1=CC=CC=C21	2427.3	Semi standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,2TMS,isomer #1	C[Si](C)(C)N1CCC2=C(C1C(Cl)(Cl)Cl)N([Si](C)(C)C)C1=CC=CC=C21	2508.3	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,2TMS,isomer #1	C[Si](C)(C)N1CCC2=C(C1C(Cl)(Cl)Cl)N([Si](C)(C)C)C1=CC=CC=C21	2561.6	Standard polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCC2=C([NH]C3=CC=CC=C23)C1C(Cl)(Cl)Cl	2590.0	Semi standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCC2=C([NH]C3=CC=CC=C23)C1C(Cl)(Cl)Cl	2631.8	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCC2=C([NH]C3=CC=CC=C23)C1C(Cl)(Cl)Cl	2960.3	Standard polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=C(CCNC2C(Cl)(Cl)Cl)C2=CC=CC=C21	2559.1	Semi standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=C(CCNC2C(Cl)(Cl)Cl)C2=CC=CC=C21	2594.6	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=C(CCNC2C(Cl)(Cl)Cl)C2=CC=CC=C21	2931.2	Standard polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCC2=C(C1C(Cl)(Cl)Cl)N([Si](C)(C)C(C)(C)C)C1=CC=CC=C21	2792.7	Semi standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCC2=C(C1C(Cl)(Cl)Cl)N([Si](C)(C)C(C)(C)C)C1=CC=CC=C21	2965.9	Standard non polar	33892256
1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1CCC2=C(C1C(Cl)(Cl)Cl)N([Si](C)(C)C(C)(C)C)C1=CC=CC=C21	2768.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dl-2900000000-739c1f747b7abdbca44f	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline GC-MS (Non-derivatized) - 70eV, Positive	Not Available	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

106473

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

119183

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 1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline (HMDB0258676)

MOL for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

3D MOL for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

3D SDF for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

3D-SDF for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

PDB for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

3D PDB for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

SMILES for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

INCHI for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

Structure for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

3D Structure for HMDB0258676 (1-Trichloromethyl-1,2,3,4-tetrahydro-beta-carboline)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra