MiMeDB: Showing metabocard for Harman (MMDBc0000671)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:52:23 UTC

Update Date

2024-10-17 15:57:56 UTC

Metabolite ID

MMDBc0000671

Metabolite Identification

Common Name

Harman

Description

Harman is found in chicory. Harman is an alkaloid from the may pop (Passiflora incarnata, Passifloraceae) and many other Passiflora sp

Structure

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


  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>
MMDBc0000671

> <DATABASE_NAME>
MIME

> <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

$$$$

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

Synonyms

Value	Source
1-Methyl-2-carboline	ChEBI
1-Methyl-9H-beta-carboline	ChEBI
1-Methyl-beta-carboline	ChEBI
1-Methylnorharman	ChEBI
Aribin	ChEBI
Aribine	ChEBI
Harmane	ChEBI
L-Methylpyridobindole	ChEBI
Locuturin	ChEBI
Locuturine	ChEBI
Loturine	ChEBI
Passiflorin	ChEBI
1-Methyl-9H-b-carboline	Generator
1-Methyl-9H-β-carboline	Generator
1-Methyl-b-carboline	Generator
1-Methyl-β-carboline	Generator
1-Methyl-9H-pyrido[3,4-b]indole	HMDB
1-Methyl-9H-pyrido[3,4-b]indole, 9ci	HMDB
2-Methyl-beta-carboline	HMDB
3-Methyl-4-carboline	HMDB
L-Methyl-pyridobindole	HMDB
Passiflorine	HMDB
Zygofabagine	HMDB
Harman hydrochloride	HMDB

Molecular Formula

C₁₂H₁₀N₂

Average Mass

182.2212

Monoisotopic Mass

182.08439833

IUPAC Name

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

Traditional Name

harmane

CAS Registry Number

Not Available

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

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
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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

indole alkaloid (CHEBI:5623 )
indole alkaloid fundamental parent (CHEBI:5623 )
harmala alkaloid (CHEBI:5623 )
Indole alkaloids (C09209 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.097 g/L	ALOGPS
logP	3.36	ALOGPS
logP	2	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	13.72	ChemAxon
pKa (Strongest Basic)	5.97	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	28.68 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	55.91 m³·mol⁻¹	ChemAxon
Polarizability	20.28 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

Spectra

Not Available

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Bacteroidetes	1	Human ; Human feces; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0035196

DrugBank ID

Not Available

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

Harman

METLIN ID

Not Available

PubChem Compound

5281404

PDB ID

Not Available

ChEBI ID

5623

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Abramets II, Dolzhenko AT: [Harman and its derivatives as potential atypical antidepressants]. Farmakol Toksikol. 1986 Jul-Aug;49(4):15-9. [PubMed:3758321 ]
Yannai, Shmuel (2004). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. Boca Raton: Chapman & Hall/CRC..

Showing metabocard for Harman (MMDBc0000671)

MOL for #<Metabolite:0x00007f91fbbcfb80>

3D MOL for #<Metabolite:0x00007f91fbbcfb80>

3D SDF for #<Metabolite:0x00007f91fbbcfb80>

3D-SDF for #<Metabolite:0x00007f91fbbcfb80>

PDB for #<Metabolite:0x00007f91fbbcfb80>

3D PDB for #<Metabolite:0x00007f91fbbcfb80>

SMILES for #<Metabolite:0x00007f91fbbcfb80>

INCHI for #<Metabolite:0x00007f91fbbcfb80>

Structure for #<Metabolite:0x00007f91fbbcfb80>

3D Structure for #<Metabolite:0x00007f91fbbcfb80>