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

2024-04-30 19:33:28 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

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-001i-4900000000-2caa4dc9ec4e3750fe94	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-001i-4900000000-2caa4dc9ec4e3750fe94	2018-05-18	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f89-0900000000-1eb823770f43aa96d079	2017-07-27	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-001i-0900000000-8a722b1b5d7b5941896b	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-001i-0900000000-c3e22e3a50c1a33d3313	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-001i-0900000000-da3abe12c596a25c4fc7	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-00lr-0900000000-a0630fe37a9dae900711	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-014i-0900000000-fe40ad28de7c40fde973	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-001i-0900000000-2c091f7fb293a5702807	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-001i-2900000000-37a11b66e75cedf3e072	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-001i-2900000000-753e83180abd8e8f4306	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-053r-4900000000-a0c45efe16d695cf0465	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-03di-2900000000-4e2e84a5d7cb4f3b6e5a	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - ESI-ITFT , negative	splash10-001i-0900000000-da5f8f71b14a2afaf96b	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-0900000000-b61926dd87fa8a8bf547	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-0900000000-be2b3d6251e5698ec184	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-0900000000-2467a87546dc5758f74c	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-014i-0900000000-6222b796373c7d683edd	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-014i-0900000000-5f9fc354bf2eb82f440c	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-0900000000-8f767ae14c8cb390abd4	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-0900000000-3206fb22991bbadfb410	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-014i-0900000000-fbe37bd173c6820a5fbf	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-0900000000-f0389c36d5ddc1a056cd	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-0900000000-f4d0d496031eda8facca	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00kf-0900000000-24a22633d62b61cf09b2	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0900000000-c6d6c9589b7c3045e05e	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-0900000000-155dea2165739f0af46e	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-067i-0900000000-78073f143aded0ccce81	2016-08-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0004278	S-Adenosylmethionine	S-Adenosylhomocysteine	Not Available		VMH	1528988

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	Firmicutes	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Bacteroidetes	1	Human ; Human feces; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

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:0x00007fd12cac8938>

3D MOL for #<Metabolite:0x00007fd12cac8938>

3D SDF for #<Metabolite:0x00007fd12cac8938>

3D-SDF for #<Metabolite:0x00007fd12cac8938>

PDB for #<Metabolite:0x00007fd12cac8938>

3D PDB for #<Metabolite:0x00007fd12cac8938>

SMILES for #<Metabolite:0x00007fd12cac8938>

INCHI for #<Metabolite:0x00007fd12cac8938>

Structure for #<Metabolite:0x00007fd12cac8938>

3D Structure for #<Metabolite:0x00007fd12cac8938>