NP-MRD: Showing NP-Card for Harmaline (NP0050874)

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Record Information

Version

2.0

Created at

2022-04-27 22:19:48 UTC

Updated at

2022-04-27 22:19:48 UTC

NP-MRD ID

NP0050874

Secondary Accession Numbers

None

Natural Product 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 very strong basic compound (based on its pKa). Outside of the human body, Harmaline has been detected, but not quantified in, fruits and herbs and spices. This could make harmaline a potential biomarker for the consumption of these foods. Harmaline is found in Banisteria caapi, Banisteriopsis caapi, Banisteriopsis caapi(Spr. Ex Briesb.), Daphnia pulex, Elaeagnus angustifolia , Oxalis tuberosa Molina , Passiflora incarnata , Passiflora pilosicorona, Peganum harmala , Perganum harmala, Psychotria viridis and Tribulus terrestris L. . Harmaline was first documented in 1977 (PMID: 918633). A harmala alkaloid in which the harman skeleton is methoxy-substituted at C-7 and has been reduced across the 3,4 bond.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 32  0  0  0  0  0  0  0  0999 V2000
    5.2957   -0.0339    0.3906 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2416    0.9084    0.4320 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9285    0.4603    0.3044 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6552   -0.8667    0.1416 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3496   -1.2989    0.0163 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2738   -0.4411    0.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0781   -0.5907   -0.0498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6462    0.6737    0.0560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6349    1.5501    0.2129 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5541    0.9018    0.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8574    1.3324    0.3370 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0843    0.7743   -0.0183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7576    2.1066    0.0888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7878   -0.2702   -0.1755 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3390   -1.6080   -0.2965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8782   -1.8231   -0.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1737   -0.5850   -0.5824 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1614   -0.8259    1.1730 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2785    0.4328    0.4013 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4583   -1.6009    0.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1305   -2.3567   -0.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8032    2.5822    0.3169 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0260    2.3787    0.4625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2835    2.6496    0.9322 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8361    1.9715    0.2527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5953    2.6642   -0.8712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8453   -2.2109    0.5129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7371   -2.0468   -1.2580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5845   -2.5216    0.5909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4933   -2.3063   -1.1763 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3 11  2  0
 11 10  1  0
 10  6  2  0
  6  5  1  0
  5  4  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
  4  3  1  0
 16  7  1  0
  9 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
 11 23  1  0
  5 21  1  0
  4 20  1  0
  9 22  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>
NP0050874

> <DATABASE_NAME>
NP-MRD

> <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

$$$$

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

View in JSmol

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 Mass

214.2631 Da

Monoisotopic Mass

214.11061 Da

IUPAC Name

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

Traditional Name

harmaline

CAS Registry Number

Not Available

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Banisteria caapi	Plant	KNApSAcK
Banisteriopsis caapi	LOTUS Database	35616633
Banisteriopsis caapi(Spr. Ex Briesb.)	Plant	KNApSAcK
Daphnia pulex	LOTUS Database	35616633
Elaeagnus angustifolia	Plant	KNApSAcK
Oxalis tuberosa Molina	Plant	KNApSAcK
Passiflora incarnata	Plant	KNApSAcK
Passiflora pilosicorona	LOTUS Database	35616633
Peganum harmala	Plant	KNApSAcK
Perganum harmala	-	KNApSAcK
Psychotria viridis	Plant	KNApSAcK
Tribulus terrestris	Plant	KNApSAcK

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 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
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