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Showing metabocard for Harman (HMDB0035196)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 20:08:43 UTC
Update Date2023-02-21 17:24:40 UTC
HMDB IDHMDB0035196
Secondary Accession Numbers
  • HMDB35196
Metabolite Identification
Common NameHarman
DescriptionHarman, also known as aribin or locuturin, 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. Harman 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 Harman.
Structure
Data?1677000280
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035196 (Harman)

  Mrv1652304272018132D          

 14 16  0  0  0  0            999 V2000
   -3.1394    1.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8783    2.1481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5457    2.6330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3857    1.4769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9645    1.3276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7182    0.9920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2994    2.2974    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6320    0.1715    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6 10  2  0  0  0  0
  7 13  2  0  0  0  0
  8 12  2  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0035196 (Harman)

HMDB0035196
     RDKit          3D
Harman
 24 26  0  0  0  0  0  0  0  0999 V2000
   -3.4526    0.8852   -0.0094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4391   -0.2004   -0.0144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7582   -1.5051   -0.0232 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8699   -2.5019   -0.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5246   -2.1982   -0.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1423   -0.8747   -0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0930    0.1227   -0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4062    1.2873   -0.0014 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9214    1.0542   -0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0439    1.8773    0.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3238    1.3675    0.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5068    0.0009   -0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4007   -0.8327   -0.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1277   -0.3006   -0.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3125    0.5670   -0.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8038    1.0046    1.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0156    1.8133   -0.4431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1688   -3.5578   -0.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2558   -2.9451   -0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8152    2.2471    0.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9148    2.9438    0.0132 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2081    2.0181    0.0114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5225   -0.3866   -0.0032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -1.8857   -0.0161 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  7  2  1  0
 14  9  1  0
 14  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  5 19  1  0
  8 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
M  END
Download

3D SDF for HMDB0035196 (Harman)

  Mrv1652304272018132D          

 14 16  0  0  0  0            999 V2000
   -3.1394    1.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8783    2.1481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5457    2.6330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3857    1.4769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9645    1.3276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7182    0.9920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2994    2.2974    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6320    0.1715    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6 10  2  0  0  0  0
  7 13  2  0  0  0  0
  8 12  2  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035196

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C2NC3=CC=CC=C3C2=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C12H10N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-7,14H,1H3

> <INCHI_KEY>
PSFDQSOCUJVVGF-UHFFFAOYSA-N

> <FORMULA>
C12H10N2

> <MOLECULAR_WEIGHT>
182.2212

> <EXACT_MASS>
182.08439833

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
20.278847936475227

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
3.36

> <JCHEM_LOGP>
2.004583431333333

> <ALOGPS_LOGS>
-3.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.71802736754174

> <JCHEM_PKA_STRONGEST_BASIC>
5.972448491323834

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
55.9068

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.67e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
harmane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0035196 (Harman)

HMDB0035196
     RDKit          3D
Harman
 24 26  0  0  0  0  0  0  0  0999 V2000
   -3.4526    0.8852   -0.0094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4391   -0.2004   -0.0144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7582   -1.5051   -0.0232 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8699   -2.5019   -0.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5246   -2.1982   -0.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1423   -0.8747   -0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0930    0.1227   -0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4062    1.2873   -0.0014 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9214    1.0542   -0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0439    1.8773    0.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3238    1.3675    0.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5068    0.0009   -0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4007   -0.8327   -0.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1277   -0.3006   -0.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3125    0.5670   -0.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8038    1.0046    1.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0156    1.8133   -0.4431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1688   -3.5578   -0.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2558   -2.9451   -0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8152    2.2471    0.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9148    2.9438    0.0132 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2081    2.0181    0.0114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5225   -0.3866   -0.0032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -1.8857   -0.0161 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  7  2  1  0
 14  9  1  0
 14  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  5 19  1  0
  8 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
M  END
Download

PDB for HMDB0035196 (Harman)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0      -5.860   2.131   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.640   4.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.885   4.915   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.453   2.757   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.800   2.478   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.207   1.852   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -4.292   4.289   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      -3.046   0.320   0.000  0.00  0.00           N+0
CONECT    1    8                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    9                                                       
CONECT    5    3   11                                                       
CONECT    6    7   10                                                       
CONECT    7    6   13                                                       
CONECT    8    1   12   13                                                  
CONECT    9    4   10   11                                                  
CONECT   10    6    9   12                                                  
CONECT   11    5    9   14                                                  
CONECT   12    8   10   14                                                  
CONECT   13    7    8                                                       
CONECT   14   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END
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3D PDB for HMDB0035196 (Harman)

COMPND    HMDB0035196
HETATM    1  C1  UNL     1      -3.453   0.885  -0.009  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.439  -0.200  -0.014  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.758  -1.505  -0.023  1.00  0.00           N  
HETATM    4  C3  UNL     1      -1.870  -2.502  -0.028  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.525  -2.198  -0.024  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.142  -0.875  -0.015  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.093   0.123  -0.010  1.00  0.00           C  
HETATM    8  N2  UNL     1      -0.406   1.287  -0.001  1.00  0.00           N  
HETATM    9  C7  UNL     1       0.921   1.054  -0.001  1.00  0.00           C  
HETATM   10  C8  UNL     1       2.044   1.877   0.007  1.00  0.00           C  
HETATM   11  C9  UNL     1       3.324   1.367   0.006  1.00  0.00           C  
HETATM   12  C10 UNL     1       3.507   0.001  -0.003  1.00  0.00           C  
HETATM   13  C11 UNL     1       2.401  -0.833  -0.010  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.128  -0.301  -0.009  1.00  0.00           C  
HETATM   15  H1  UNL     1      -4.312   0.567  -0.644  1.00  0.00           H  
HETATM   16  H2  UNL     1      -3.804   1.005   1.022  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.016   1.813  -0.443  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.169  -3.558  -0.035  1.00  0.00           H  
HETATM   19  H5  UNL     1       0.256  -2.945  -0.027  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.815   2.247   0.004  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.915   2.944   0.013  1.00  0.00           H  
HETATM   22  H8  UNL     1       4.208   2.018   0.011  1.00  0.00           H  
HETATM   23  H9  UNL     1       4.523  -0.387  -0.003  1.00  0.00           H  
HETATM   24  H10 UNL     1       2.576  -1.886  -0.016  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   18
CONECT    5    6   19
CONECT    6    7    7   14
CONECT    7    8
CONECT    8    9   20
CONECT    9   10   10   14
CONECT   10   11   21
CONECT   11   12   12   22
CONECT   12   13   23
CONECT   13   14   14   24
END
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SMILES for HMDB0035196 (Harman)

CC1=C2NC3=CC=CC=C3C2=CC=N1
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INCHI for HMDB0035196 (Harman)

InChI=1S/C12H10N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-7,14H,1H3
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC12H10N2
Average Molecular Weight182.2212
Monoisotopic Molecular Weight182.08439833
IUPAC Name1-methyl-9H-pyrido[3,4-b]indole
Traditional Nameharmane
CAS Registry Number486-84-0
SMILES
CC1=C2NC3=CC=CC=C3C2=CC=N1
InChI Identifier
InChI=1S/C12H10N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-7,14H,1H3
InChI KeyPSFDQSOCUJVVGF-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.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassHarmala alkaloids
Sub ClassNot Available
Direct ParentHarmala alkaloids
Alternative Parents
Substituents
  • Harman
  • Beta-carboline
  • Pyridoindole
  • Indole
  • Indole or derivatives
  • Methylpyridine
  • Pyridine
  • Benzenoid
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point237 - 238 °CNot Available
Boiling Point386.90 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility9.39 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP3.10Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available136.631http://allccs.zhulab.cn/database/detail?ID=AllCCS00001377
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021482
KNApSAcK IDC00001736
Chemspider ID4444755
KEGG Compound IDC09209
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHarman
METLIN IDNot Available
PubChem Compound5281404
PDB IDNot Available
ChEBI ID5623
Food Biomarker OntologyNot Available
VMH IDC09209
MarkerDB IDNot Available
Good Scents IDrw1249091
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Abramets II, Dolzhenko AT: [Harman and its derivatives as potential atypical antidepressants]. Farmakol Toksikol. 1986 Jul-Aug;49(4):15-9. [PubMed:3758321 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .