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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:36:03 UTC

Update Date

2022-03-07 02:52:30 UTC

HMDB ID

HMDB0030310

Secondary Accession Numbers

HMDB30310

Metabolite Identification

Common Name

Harmaline

Description

Harmaline, also known as dihydroharmine or harmidine, 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. Harmaline is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Harmaline.

Structure

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

HMDB0030310
     RDKit          3D
Harmaline
 30 32  0  0  0  0  0  0  0  0999 V2000
    5.3056   -0.2973   -0.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1760   -1.1144   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8781   -0.6259   -0.2867 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6934    0.7365   -0.3938 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4072    1.2364   -0.3652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2919    0.4209   -0.2329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0672    0.6472   -0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6732   -0.5780   -0.0374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199   -1.5208   -0.0093 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4993   -0.9516   -0.1262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7874   -1.4570   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1331   -0.5832    0.0454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8630   -1.8804    0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7668    0.5107   -0.0126 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2603    1.8353   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7870    1.9354   -0.2487 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4648    0.0910   -1.4728 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2717    0.6060    0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2220   -0.8469   -0.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5380    1.4029   -0.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2336    2.3068   -0.4477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8997   -2.5499    0.0893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9546   -2.5157   -0.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9093   -1.6943    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4131   -2.5169    0.9878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8878   -2.3754   -0.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7866    2.3467   -0.9955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5970    2.4203    0.7561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4151    2.6405    0.5549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5446    2.3708   -1.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  1  0
 10 11  2  0
  8 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
 11  3  1  0
 10  6  1  0
 16  7  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  5 21  1  0
  9 22  1  0
 11 23  1  0
 13 24  1  0
 13 25  1  0
 13 26  1  0
 15 27  1  0
 15 28  1  0
 16 29  1  0
 16 30  1  0
M  END


  Mrv0541 05061305092D          

 16 18  0  0  0  0            999 V2000
    0.2046   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3194    0.6825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7674    0.0694    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  6  5  1  0  0  0  0
  8  1  1  0  0  0  0
  9  3  1  0  0  0  0
  9  7  2  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  1  0  0  0  0
 13 11  2  0  0  0  0
 14  6  1  0  0  0  0
 14  8  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16  2  1  0  0  0  0
 16  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030310

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC1

> <INCHI_IDENTIFIER>
InChI=1S/C13H14N2O/c1-8-13-11(5-6-14-8)10-4-3-9(16-2)7-12(10)15-13/h3-4,7,15H,5-6H2,1-2H3

> <INCHI_KEY>
RERZNCLIYCABFS-UHFFFAOYSA-N

> <FORMULA>
C13H14N2O

> <MOLECULAR_WEIGHT>
214.2631

> <EXACT_MASS>
214.11061308

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
24.199848953968377

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-methoxy-1-methyl-3H,4H,9H-pyrido[3,4-b]indole

> <ALOGPS_LOGP>
2.61

> <JCHEM_LOGP>
1.668211271

> <ALOGPS_LOGS>
-3.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.954947232010259

> <JCHEM_PKA_STRONGEST_BASIC>
6.462843260482312

> <JCHEM_POLAR_SURFACE_AREA>
37.379999999999995

> <JCHEM_REFRACTIVITY>
64.1514

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.76e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
harmaline

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0030310
     RDKit          3D
Harmaline
 30 32  0  0  0  0  0  0  0  0999 V2000
    5.3056   -0.2973   -0.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1760   -1.1144   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8781   -0.6259   -0.2867 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6934    0.7365   -0.3938 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4072    1.2364   -0.3652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2919    0.4209   -0.2329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0672    0.6472   -0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6732   -0.5780   -0.0374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199   -1.5208   -0.0093 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4993   -0.9516   -0.1262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7874   -1.4570   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1331   -0.5832    0.0454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8630   -1.8804    0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7668    0.5107   -0.0126 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2603    1.8353   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7870    1.9354   -0.2487 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4648    0.0910   -1.4728 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2717    0.6060    0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2220   -0.8469   -0.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5380    1.4029   -0.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2336    2.3068   -0.4477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8997   -2.5499    0.0893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9546   -2.5157   -0.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9093   -1.6943    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4131   -2.5169    0.9878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8878   -2.3754   -0.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7866    2.3467   -0.9955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5970    2.4203    0.7561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4151    2.6405    0.5549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5446    2.3708   -1.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  1  0
 10 11  2  0
  8 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
 11  3  1  0
 10  6  1  0
 16  7  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  5 21  1  0
  9 22  1  0
 11 23  1  0
 13 24  1  0
 13 25  1  0
 13 26  1  0
 15 27  1  0
 15 28  1  0
 16 29  1  0
 16 30  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       0.382  -2.159   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.930   1.274   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.411   2.235   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.393   0.450   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -0.173   0.450   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       8.899   0.130   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2   16                                                            
CONECT    3    4    9                                                       
CONECT    4    3   10                                                       
CONECT    5    6   11                                                       
CONECT    6    5   14                                                       
CONECT    7    9   12                                                       
CONECT    8    1   13   14                                                  
CONECT    9    3    7   16                                                  
CONECT   10    4   11   12                                                  
CONECT   11    5   10   13                                                  
CONECT   12    7   10   15                                                  
CONECT   13    8   11   15                                                  
CONECT   14    6    8                                                       
CONECT   15   12   13                                                       
CONECT   16    2    9                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

COMPND    HMDB0030310
HETATM    1  C1  UNL     1       5.306  -0.297  -0.450  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.176  -1.114  -0.317  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.878  -0.626  -0.287  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.693   0.737  -0.394  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.407   1.236  -0.365  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.292   0.421  -0.233  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.067   0.647  -0.177  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.673  -0.578  -0.037  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.720  -1.521  -0.009  1.00  0.00           N  
HETATM   10  C8  UNL     1       0.499  -0.952  -0.126  1.00  0.00           C  
HETATM   11  C9  UNL     1       1.787  -1.457  -0.154  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.133  -0.583   0.045  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.863  -1.880   0.198  1.00  0.00           C  
HETATM   14  N2  UNL     1      -3.767   0.511  -0.013  1.00  0.00           N  
HETATM   15  C12 UNL     1      -3.260   1.835  -0.154  1.00  0.00           C  
HETATM   16  C13 UNL     1      -1.787   1.935  -0.249  1.00  0.00           C  
HETATM   17  H1  UNL     1       5.465   0.091  -1.473  1.00  0.00           H  
HETATM   18  H2  UNL     1       5.272   0.606   0.220  1.00  0.00           H  
HETATM   19  H3  UNL     1       6.222  -0.847  -0.126  1.00  0.00           H  
HETATM   20  H4  UNL     1       3.538   1.403  -0.498  1.00  0.00           H  
HETATM   21  H5  UNL     1       1.234   2.307  -0.448  1.00  0.00           H  
HETATM   22  H6  UNL     1      -0.900  -2.550   0.089  1.00  0.00           H  
HETATM   23  H7  UNL     1       1.955  -2.516  -0.073  1.00  0.00           H  
HETATM   24  H8  UNL     1      -4.909  -1.694   0.497  1.00  0.00           H  
HETATM   25  H9  UNL     1      -3.413  -2.517   0.988  1.00  0.00           H  
HETATM   26  H10 UNL     1      -3.888  -2.375  -0.795  1.00  0.00           H  
HETATM   27  H11 UNL     1      -3.787   2.347  -0.995  1.00  0.00           H  
HETATM   28  H12 UNL     1      -3.597   2.420   0.756  1.00  0.00           H  
HETATM   29  H13 UNL     1      -1.415   2.641   0.555  1.00  0.00           H  
HETATM   30  H14 UNL     1      -1.545   2.371  -1.247  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3
CONECT    3    4    4   11
CONECT    4    5   20
CONECT    5    6    6   21
CONECT    6    7   10
CONECT    7    8    8   16
CONECT    8    9   12
CONECT    9   10   22
CONECT   10   11   11
CONECT   11   23
CONECT   12   13   14   14
CONECT   13   24   25   26
CONECT   14   15
CONECT   15   16   27   28
CONECT   16   29   30
END

HMDB0030310
     RDKit          3D
Harmaline
 30 32  0  0  0  0  0  0  0  0999 V2000
    5.3056   -0.2973   -0.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1760   -1.1144   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8781   -0.6259   -0.2867 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6934    0.7365   -0.3938 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4072    1.2364   -0.3652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2919    0.4209   -0.2329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0672    0.6472   -0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6732   -0.5780   -0.0374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199   -1.5208   -0.0093 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4993   -0.9516   -0.1262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7874   -1.4570   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1331   -0.5832    0.0454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8630   -1.8804    0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7668    0.5107   -0.0126 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2603    1.8353   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7870    1.9354   -0.2487 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4648    0.0910   -1.4728 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2717    0.6060    0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2220   -0.8469   -0.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5380    1.4029   -0.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2336    2.3068   -0.4477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8997   -2.5499    0.0893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9546   -2.5157   -0.0726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9093   -1.6943    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4131   -2.5169    0.9878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8878   -2.3754   -0.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7866    2.3467   -0.9955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5970    2.4203    0.7561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4151    2.6405    0.5549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5446    2.3708   -1.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  1  0
 10 11  2  0
  8 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
 11  3  1  0
 10  6  1  0
 16  7  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  5 21  1  0
  9 22  1  0
 11 23  1  0
 13 24  1  0
 13 25  1  0
 13 26  1  0
 15 27  1  0
 15 28  1  0
 16 29  1  0
 16 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,4-Dihydroharmine	ChEBI
7-Methoxy-1-methyl-4,9-dihydro-3H-beta-carboline	ChEBI
Armalin	ChEBI
Dihydroharmine	ChEBI
Harmalin	ChEBI
Harmalol methyl ether	ChEBI
Harmidine	ChEBI
O-Methylharmalol	ChEBI
7-Methoxy-1-methyl-4,9-dihydro-3H-b-carboline	Generator
7-Methoxy-1-methyl-4,9-dihydro-3H-β-carboline	Generator
1-Methyl-7-methoxy-3, 4-dihydro-beta -carboline	HMDB
1-Methyl-7-methoxy-3,4-dihydro- beta-carboline	HMDB
1-Methyl-7-methoxy-3,4-dihydro-beta -carboline	HMDB
1-Methyl-7-methoxy-3,4-dihydro-beta-carboline	HMDB
3, 4-Dihydroharmine	HMDB
3,4-Dihydro-7-methoxy-1-methyl-9-pyrid(3,4-b)indole	HMDB
3,4-Dihydro-7-methoxy-1-methyl-9-pyrido(3,4-b)indole	HMDB
3,4-Dihydro-7-methoxy-1-methyl-9-pyrid[3,4-b]indole	HMDB
3,4-Dihydro-7-methoxy-1-methyl-b-carboline	HMDB
4,9-Dihydro-7-methoxy-1-methyl-3H-pyrido(3,4-b)indole	HMDB
4,9-Dihydro-7-methoxy-1-methyl-3H-pyrido[3,4-b]indole	HMDB
Dihydro-harmine	HMDB

Chemical Formula

C₁₃H₁₄N₂O

Average Molecular Weight

214.2631

Monoisotopic Molecular Weight

214.11061308

IUPAC Name

7-methoxy-1-methyl-3H,4H,9H-pyrido[3,4-b]indole

Traditional Name

harmaline

CAS Registry Number

304-21-2

SMILES

COC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC1

InChI Identifier

InChI=1S/C13H14N2O/c1-8-13-11(5-6-14-8)10-4-3-9(16-2)7-12(10)15-13/h3-4,7,15H,5-6H2,1-2H3

InChI Key

RERZNCLIYCABFS-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

Harmaline
Harman
Beta-carboline
Pyridoindole
3-alkylindole
Indole or derivatives
Indole
Anisole
Alkyl aryl ether
Benzenoid
Heteroaromatic compound
Pyrrole
Ketimine
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Ether
Organopnictogen compound
Imine
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

harmala alkaloid (CHEBI:28172 )
Indole alkaloids (C06536 )
an alkaloid (CPD-9939 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	250 - 251 °C	Not Available
Boiling Point	426.42 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	4.05 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	2.251 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	146.183	http://allccs.zhulab.cn/database/detail?ID=AllCCS00001376

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.058 g/L	ALOGPS
logP	2.61	ALOGPS
logP	1.67	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	14.95	ChemAxon
pKa (Strongest Basic)	6.46	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.38 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	64.15 m³·mol⁻¹	ChemAxon
Polarizability	24.2 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
DarkChem	[M+H]+	150.474	31661259
DarkChem	[M-H]-	149.335	31661259
DeepCCS	[M+H]+	155.559	30932474
DeepCCS	[M-H]-	153.201	30932474
DeepCCS	[M-2H]-	186.087	30932474
DeepCCS	[M+Na]+	161.652	30932474
AllCCS	[M+H]+	147.5	32859911
AllCCS	[M+H-H2O]+	143.3	32859911
AllCCS	[M+NH4]+	151.4	32859911
AllCCS	[M+Na]+	152.6	32859911
AllCCS	[M-H]-	154.3	32859911
AllCCS	[M+Na-2H]-	154.1	32859911
AllCCS	[M+HCOO]-	154.1	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. Predicted by Afia on May 17, 2022.	4.3 minutes	32390414
Predicted by Siyang on May 30, 2022	11.5859 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.99 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	29.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1526.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	345.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	144.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	194.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	127.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	433.1 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	376.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	113.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	823.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	402.7 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	1087.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	234.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	314.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	390.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	245.7 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	20.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Harmaline	COC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC1	2938.9	Standard polar	33892256
Harmaline	COC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC1	2093.4	Standard non polar	33892256
Harmaline	COC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC1	2287.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Harmaline,1TMS,isomer #1	COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C)C2=C1	2260.2	Semi standard non polar	33892256
Harmaline,1TMS,isomer #1	COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C)C2=C1	2076.2	Standard non polar	33892256
Harmaline,1TBDMS,isomer #1	COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C(C)(C)C)C2=C1	2453.6	Semi standard non polar	33892256
Harmaline,1TBDMS,isomer #1	COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C(C)(C)C)C2=C1	2312.1	Standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB13875

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Harmaline

METLIN ID

Not Available

PubChem Compound

3564

PDB ID

Not Available

ChEBI ID

28172

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1249071

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

de Sousa RC: [The cell membrane: a frontier between 2 worlds]. Schweiz Med Wochenschr. 1977 Nov 12;107(45):1605-12. [PubMed:918633 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Harmaline (HMDB0030310)

MOL for HMDB0030310 (Harmaline)

3D MOL for HMDB0030310 (Harmaline)

3D SDF for HMDB0030310 (Harmaline)

3D-SDF for HMDB0030310 (Harmaline)

PDB for HMDB0030310 (Harmaline)

3D PDB for HMDB0030310 (Harmaline)

SMILES for HMDB0030310 (Harmaline)

INCHI for HMDB0030310 (Harmaline)

Structure for HMDB0030310 (Harmaline)

3D Structure for HMDB0030310 (Harmaline)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized