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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:36:03 UTC
Update Date2021-10-13 06:07:12 UTC
HMDB IDHMDB0030310
Secondary Accession Numbers
  • HMDB30310
Metabolite Identification
Common NameHarmaline
DescriptionHarmaline, 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
Data?1563861967
Synonyms
ValueSource
3,4-DihydroharmineChEBI
7-Methoxy-1-methyl-4,9-dihydro-3H-beta-carbolineChEBI
ArmalinChEBI
DihydroharmineChEBI
HarmalinChEBI
Harmalol methyl etherChEBI
HarmidineChEBI
O-MethylharmalolChEBI
7-Methoxy-1-methyl-4,9-dihydro-3H-b-carbolineGenerator
7-Methoxy-1-methyl-4,9-dihydro-3H-β-carbolineGenerator
1-Methyl-7-methoxy-3, 4-dihydro-beta -carbolineHMDB
1-Methyl-7-methoxy-3,4-dihydro- beta-carbolineHMDB
1-Methyl-7-methoxy-3,4-dihydro-beta -carbolineHMDB
1-Methyl-7-methoxy-3,4-dihydro-beta-carbolineHMDB
3, 4-DihydroharmineHMDB
3,4-Dihydro-7-methoxy-1-methyl-9-pyrid(3,4-b)indoleHMDB
3,4-Dihydro-7-methoxy-1-methyl-9-pyrido(3,4-b)indoleHMDB
3,4-Dihydro-7-methoxy-1-methyl-9-pyrid[3,4-b]indoleHMDB
3,4-Dihydro-7-methoxy-1-methyl-b-carbolineHMDB
4,9-Dihydro-7-methoxy-1-methyl-3H-pyrido(3,4-b)indoleHMDB
4,9-Dihydro-7-methoxy-1-methyl-3H-pyrido[3,4-b]indoleHMDB
Dihydro-harmineHMDB
Chemical FormulaC13H14N2O
Average Molecular Weight214.2631
Monoisotopic Molecular Weight214.11061308
IUPAC Name7-methoxy-1-methyl-3H,4H,9H-pyrido[3,4-b]indole
Traditional Nameharmaline
CAS Registry Number304-21-2
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 KeyRERZNCLIYCABFS-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
  • 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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point250 - 251 °CNot Available
Boiling Point426.42 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility4.05 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.251 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available146.183http://allccs.zhulab.cn/database/detail?ID=AllCCS00001376
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.058 g/LALOGPS
logP10(2.61) g/LALOGPS
logP10(1.67) g/LChemAxon
logS10(-3.6) g/LALOGPS
pKa (Strongest Acidic)14.95ChemAxon
pKa (Strongest Basic)6.46ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.38 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity64.15 m³·mol⁻¹ChemAxon
Polarizability24.2 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+150.47431661259
DarkChem[M-H]-149.33531661259

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
HarmalineCOC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC12938.9Standard polar33892256
HarmalineCOC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC12093.4Standard non polar33892256
HarmalineCOC1=CC2=C(C=C1)C1=C(N2)C(C)=NCC12287.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Harmaline,1TMS,isomer #1COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C)C2=C12260.2Semi standard non polar33892256
Harmaline,1TMS,isomer #1COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C)C2=C12076.2Standard non polar33892256
Harmaline,1TBDMS,isomer #1COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C(C)(C)C)C2=C12453.6Semi standard non polar33892256
Harmaline,1TBDMS,isomer #1COC1=CC=C2C3=C(C(C)=NCC3)N([Si](C)(C)C(C)(C)C)C2=C12312.1Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Harmaline GC-MS (Non-derivatized) - 70eV, Positivesplash10-006t-0900000000-8b0bbd88d925dd13fd022017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Harmaline GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Harmaline LC-ESI-qTof , Positive-QTOFsplash10-00di-2920000000-44473ef3fbb78c164b212017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Harmaline , positive-QTOFsplash10-00di-2920000000-44473ef3fbb78c164b212017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 10V, Positive-QTOFsplash10-014i-0390000000-7a3eeedc85dd196eda222016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 20V, Positive-QTOFsplash10-014i-1970000000-c7d3b2a8e9d823519fa42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 40V, Positive-QTOFsplash10-006x-0900000000-c887581b709fc57e530f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 10V, Negative-QTOFsplash10-03di-0190000000-f7b71eafff989f1460512016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 20V, Negative-QTOFsplash10-03di-0390000000-3ce7a76fb334f9e591c52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 40V, Negative-QTOFsplash10-05nb-1900000000-35911c2afac691df4c3a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 10V, Negative-QTOFsplash10-03di-0090000000-f58ebef816fc4a8a6e352021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 20V, Negative-QTOFsplash10-03di-0490000000-59b458e2ccd967f79f652021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 40V, Negative-QTOFsplash10-00l2-0900000000-6ad9c9837aa70579242b2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 10V, Positive-QTOFsplash10-014i-0090000000-011b2ae80d93d1a6c9382021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 20V, Positive-QTOFsplash10-014i-0090000000-011b2ae80d93d1a6c9382021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Harmaline 40V, Positive-QTOFsplash10-022a-1930000000-d1f321217affc513671d2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB13875
Phenol Explorer Compound IDNot Available
FooDB IDFDB002148
KNApSAcK IDC00001735
Chemspider ID10211258
KEGG Compound IDC06536
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHarmaline
METLIN IDNot Available
PubChem Compound3564
PDB IDNot Available
ChEBI ID28172
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1249071
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. de Sousa RC: [The cell membrane: a frontier between 2 worlds]. Schweiz Med Wochenschr. 1977 Nov 12;107(45):1605-12. [PubMed:918633 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .