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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:32:57 UTC

Update Date

2023-02-21 17:19:18 UTC

HMDB ID

HMDB0029834

Secondary Accession Numbers

HMDB29834

Metabolite Identification

Common Name

Harmalan

Description

Harmalan, also known as dihydroharman, 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. Based on a literature review a small amount of articles have been published on Harmalan.

Structure

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


  Mrv1652304272018502D          

 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  1  0  0  0  0
  7 13  1  0  0  0  0
  8 12  1  0  0  0  0
  8 13  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  2  0  0  0  0
 11 14  1  0  0  0  0
 12 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029834

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=NCCC2=C1NC1=CC=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C12H12N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-5,14H,6-7H2,1H3

> <INCHI_KEY>
CWOYLIJQLSNRRN-UHFFFAOYSA-N

> <FORMULA>
C12H12N2

> <MOLECULAR_WEIGHT>
184.2371

> <EXACT_MASS>
184.100048394

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
21.012017662052266

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.64

> <JCHEM_LOGP>
1.8258825366666662

> <ALOGPS_LOGS>
-3.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.035932239124566

> <JCHEM_PKA_STRONGEST_BASIC>
8.34106427447378

> <JCHEM_POLAR_SURFACE_AREA>
28.15

> <JCHEM_REFRACTIVITY>
57.6882

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.11e-02 g/l

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

> <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

COMPND    HMDB0029834
HETATM    1  C1  UNL     1      -2.906   2.034   0.404  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.278   0.702   0.136  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.950  -0.355  -0.080  1.00  0.00           N  
HETATM    4  C3  UNL     1      -2.467  -1.663  -0.343  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.000  -1.849  -0.377  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.199  -0.638  -0.130  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.813   0.572   0.113  1.00  0.00           C  
HETATM    8  N2  UNL     1       0.188   1.459   0.296  1.00  0.00           N  
HETATM    9  C7  UNL     1       1.381   0.848   0.175  1.00  0.00           C  
HETATM   10  C8  UNL     1       2.663   1.344   0.279  1.00  0.00           C  
HETATM   11  C9  UNL     1       3.747   0.494   0.110  1.00  0.00           C  
HETATM   12  C10 UNL     1       3.548  -0.846  -0.162  1.00  0.00           C  
HETATM   13  C11 UNL     1       2.258  -1.345  -0.266  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.175  -0.502  -0.098  1.00  0.00           C  
HETATM   15  H1  UNL     1      -3.705   1.943   1.188  1.00  0.00           H  
HETATM   16  H2  UNL     1      -3.313   2.490  -0.512  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.142   2.725   0.803  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.926  -1.989  -1.323  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.933  -2.345   0.424  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.711  -2.649   0.340  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.693  -2.257  -1.384  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.014   2.476   0.501  1.00  0.00           H  
HETATM   23  H9  UNL     1       2.884   2.387   0.491  1.00  0.00           H  
HETATM   24  H10 UNL     1       4.753   0.901   0.195  1.00  0.00           H  
HETATM   25  H11 UNL     1       4.365  -1.540  -0.300  1.00  0.00           H  
HETATM   26  H12 UNL     1       2.087  -2.397  -0.480  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7    7   14
CONECT    7    8
CONECT    8    9   22
CONECT    9   10   10   14
CONECT   10   11   23
CONECT   11   12   12   24
CONECT   12   13   25
CONECT   13   14   14   26
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Methyl-3,4-dihydro-beta-carboline	HMDB
1-Methyl-4,9-dihydro-3H-beta-carboline	HMDB
3,4-Dihydro-1-methyl-2H-pyrido[3,4-b]indole	HMDB
4,9-Dihydro-1-methyl-3H-pyrido(3,4-b)indole	HMDB
4,9-Dihydro-1-methyl-3H-pyrido[3,4-b]indole, 9ci	HMDB
Dihydroharman	HMDB

Chemical Formula

C₁₂H₁₂N₂

Average Molecular Weight

184.2371

Monoisotopic Molecular Weight

184.100048394

IUPAC Name

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

Traditional Name

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

CAS Registry Number

525-41-7

SMILES

CC1=NCCC2=C1NC1=CC=CC=C21

InChI Identifier

InChI=1S/C12H12N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-5,14H,6-7H2,1H3

InChI Key

CWOYLIJQLSNRRN-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
3-alkylindole
Indole
Indole or derivatives
Benzenoid
Heteroaromatic compound
Pyrrole
Ketimine
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organoheterocyclic compound
Azacycle
Hydrocarbon derivative
Organonitrogen compound
Organic nitrogen compound
Imine
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0029834)
Cell membrane (HMDB: HMDB0029834)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029834)

Source

Endogenous

Endogenous (HMDB: HMDB0029834)

Plant

Plant (HMDB: HMDB0029834)

Exogenous

Food

Food (HMDB: HMDB0029834)

Fruit

Fruits (FooDB: FOOD00871)

Exogenous (HMDB: HMDB0029834)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	183 - 185 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.091 g/L	ALOGPS
logP	2.64	ALOGPS
logP	1.83	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	15.04	ChemAxon
pKa (Strongest Basic)	8.34	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	28.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	57.69 m³·mol⁻¹	ChemAxon
Polarizability	21.01 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	143.109	31661259
DarkChem	[M-H]-	140.528	31661259
DeepCCS	[M+H]+	139.145	30932474
DeepCCS	[M-H]-	136.603	30932474
DeepCCS	[M-2H]-	172.275	30932474
DeepCCS	[M+Na]+	147.813	30932474
AllCCS	[M+H]+	138.8	32859911
AllCCS	[M+H-H2O]+	134.2	32859911
AllCCS	[M+NH4]+	143.0	32859911
AllCCS	[M+Na]+	144.2	32859911
AllCCS	[M-H]-	144.5	32859911
AllCCS	[M+Na-2H]-	144.4	32859911
AllCCS	[M+HCOO]-	144.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	4.14 minutes	32390414
Predicted by Siyang on May 30, 2022	11.4128 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.72 minutes	32390414

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Harmalan	CC1=NCCC2=C1NC1=C2C=CC=C1	2734.9	Standard polar	33892256
Harmalan	CC1=NCCC2=C1NC1=C2C=CC=C1	1876.9	Standard non polar	33892256
Harmalan	CC1=NCCC2=C1NC1=C2C=CC=C1	1994.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Harmalan,1TMS,isomer #1	CC1=NCCC2=C1N([Si](C)(C)C)C1=CC=CC=C21	2063.2	Semi standard non polar	33892256
Harmalan,1TMS,isomer #1	CC1=NCCC2=C1N([Si](C)(C)C)C1=CC=CC=C21	1857.1	Standard non polar	33892256
Harmalan,1TBDMS,isomer #1	CC1=NCCC2=C1N([Si](C)(C)C(C)(C)C)C1=CC=CC=C21	2274.6	Semi standard non polar	33892256
Harmalan,1TBDMS,isomer #1	CC1=NCCC2=C1N([Si](C)(C)C(C)(C)C)C1=CC=CC=C21	2106.5	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Harmalan GC-MS (Non-derivatized) - 70eV, Positive	splash10-0aou-0900000000-f4e44830fc68268ca1d4	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Harmalan GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Harmalan LC-ESI-qTof , Positive-QTOF	splash10-00kf-0900000000-cac9e8af853ce6d05f91	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Harmalan , positive-QTOF	splash10-00kf-0900000000-cac9e8af853ce6d05f91	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 10V, Positive-QTOF	splash10-000i-0900000000-c2f098f419ec8b43341a	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 20V, Positive-QTOF	splash10-000i-0900000000-0f35bce7fc33f4f2d24a	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 40V, Positive-QTOF	splash10-0006-1900000000-b6f1364180703f74b043	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 10V, Negative-QTOF	splash10-001i-0900000000-5b807ce1861cae768c7b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 20V, Negative-QTOF	splash10-001i-0900000000-f78325499d14762d4fff	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 40V, Negative-QTOF	splash10-07vl-2900000000-bfbe18f400c46178f3a4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 10V, Negative-QTOF	splash10-001i-0900000000-8d15c8b43a2a4b2520b4	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 20V, Negative-QTOF	splash10-001i-0900000000-8d15c8b43a2a4b2520b4	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 40V, Negative-QTOF	splash10-00lu-0900000000-23cb6182b1f2e7d5f88e	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 10V, Positive-QTOF	splash10-000i-0900000000-841022a695ed33826691	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 20V, Positive-QTOF	splash10-000i-0900000000-f5ea68ba19a0a333dce0	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Harmalan 40V, Positive-QTOF	splash10-00mo-2900000000-18a09d2aeb50b46cb573	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001049

KNApSAcK ID

C00054103

Chemspider ID

10309487

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

160510

PDB ID

Not Available

ChEBI ID

168990

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Harmalan (HMDB0029834)

MOL for HMDB0029834 (Harmalan)

3D MOL for HMDB0029834 (Harmalan)

3D SDF for HMDB0029834 (Harmalan)

3D-SDF for HMDB0029834 (Harmalan)

PDB for HMDB0029834 (Harmalan)

3D PDB for HMDB0029834 (Harmalan)

SMILES for HMDB0029834 (Harmalan)

INCHI for HMDB0029834 (Harmalan)

Structure for HMDB0029834 (Harmalan)

3D Structure for HMDB0029834 (Harmalan)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra