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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:36:18 UTC

Update Date

2023-02-21 17:28:31 UTC

HMDB ID

HMDB0040973

Secondary Accession Numbers

HMDB40973

Metabolite Identification

Common Name

1-Methoxy-1H-indole-3-acetonitrile

Description

1-Methoxy-1H-indole-3-acetonitrile belongs to the class of organic compounds known as 3-alkylindoles. 3-alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. 1-Methoxy-1H-indole-3-acetonitrile has been detected, but not quantified in, brassicas and chinese cabbages (Brassica rapa). This could make 1-methoxy-1H-indole-3-acetonitrile a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1-Methoxy-1H-indole-3-acetonitrile.

Structure

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


  Mrv0541 05061312172D          

 14 15  0  0  0  0            999 V2000
    1.4358    3.5881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9878   -1.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  7  6  1  0  0  0  0
  9  6  1  0  0  0  0
  9  8  2  0  0  0  0
 10  4  2  0  0  0  0
 10  9  1  0  0  0  0
 11  5  2  0  0  0  0
 11 10  1  0  0  0  0
 12  7  3  0  0  0  0
 13  8  1  0  0  0  0
 13 11  1  0  0  0  0
 14  1  1  0  0  0  0
 14 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040973

> <DATABASE_NAME>
hmdb

> <SMILES>
CON1C=C(CC#N)C2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C11H10N2O/c1-14-13-8-9(6-7-12)10-4-2-3-5-11(10)13/h2-5,8H,6H2,1H3

> <INCHI_KEY>
LIJIPBYXIXTNLE-UHFFFAOYSA-N

> <FORMULA>
C11H10N2O

> <MOLECULAR_WEIGHT>
186.2099

> <EXACT_MASS>
186.079312952

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
19.723331188225142

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(1-methoxy-1H-indol-3-yl)acetonitrile

> <ALOGPS_LOGP>
2.58

> <JCHEM_LOGP>
1.4733606430000001

> <ALOGPS_LOGS>
-2.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.413077279765723

> <JCHEM_PKA_STRONGEST_BASIC>
-4.5875660789985

> <JCHEM_POLAR_SURFACE_AREA>
37.95

> <JCHEM_REFRACTIVITY>
55.089

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.26e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(1-methoxyindol-3-yl)acetonitrile

> <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       2.680   6.698   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.680  -1.012   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.711  -2.157   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       1.650   5.553   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2   10                                                       
CONECT    5    3   11                                                       
CONECT    6    7    9                                                       
CONECT    7    6   12                                                       
CONECT    8    9   13                                                       
CONECT    9    6    8   10                                                  
CONECT   10    4    9   11                                                  
CONECT   11    5   10   13                                                  
CONECT   12    7                                                            
CONECT   13    8   11   14                                                  
CONECT   14    1   13                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Methoxy-1H-indole-3-acetonitrile, 9ci	HMDB
1-Methoxyindoleacetonitrile	HMDB
Caulilexin C	MeSH

Chemical Formula

C₁₁H₁₀N₂O

Average Molecular Weight

186.2099

Monoisotopic Molecular Weight

186.079312952

IUPAC Name

2-(1-methoxy-1H-indol-3-yl)acetonitrile

Traditional Name

2-(1-methoxyindol-3-yl)acetonitrile

CAS Registry Number

30536-48-2

SMILES

CON1C=C(CC#N)C2=CC=CC=C12

InChI Identifier

InChI=1S/C11H10N2O/c1-14-13-8-9(6-7-12)10-4-2-3-5-11(10)13/h2-5,8H,6H2,1H3

InChI Key

LIJIPBYXIXTNLE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Azacycle
Nitrile
Carbonitrile
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen 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: HMDB0040973)
Cell membrane (HMDB: HMDB0040973)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040973)

Source

Exogenous

Exogenous (HMDB: HMDB0040973)

Food

Food (HMDB: HMDB0040973)

Vegetable

Cabbage

Chinese cabbage (FooDB: FOOD00035)

Brassica

Brassicas (FooDB: FOOD00857)

Endogenous

Plant

Plant (HMDB: HMDB0040973)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040973)

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.43 g/L	ALOGPS
logP	2.58	ALOGPS
logP	1.47	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	13.41	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	37.95 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.09 m³·mol⁻¹	ChemAxon
Polarizability	19.72 Å³	ChemAxon
Number of Rings	2	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]+	140.884	31661259
DarkChem	[M-H]-	139.53	31661259
DeepCCS	[M-2H]-	169.589	30932474
DeepCCS	[M+Na]+	145.128	30932474
AllCCS	[M+H]+	139.3	32859911
AllCCS	[M+H-H2O]+	135.0	32859911
AllCCS	[M+NH4]+	143.4	32859911
AllCCS	[M+Na]+	144.6	32859911
AllCCS	[M-H]-	141.1	32859911
AllCCS	[M+Na-2H]-	141.2	32859911
AllCCS	[M+HCOO]-	141.5	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.	3.69 minutes	32390414
Predicted by Siyang on May 30, 2022	14.0646 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.69 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2261.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	499.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	173.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	300.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	272.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	550.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	670.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	116.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1135.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	423.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1402.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	360.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	350.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	450.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	372.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	24.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-Methoxy-1H-indole-3-acetonitrile	CON1C=C(CC#N)C2=CC=CC=C12	2834.8	Standard polar	33892256
1-Methoxy-1H-indole-3-acetonitrile	CON1C=C(CC#N)C2=CC=CC=C12	1708.8	Standard non polar	33892256
1-Methoxy-1H-indole-3-acetonitrile	CON1C=C(CC#N)C2=CC=CC=C12	1788.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-0900000000-179a059432ad7520a37f	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 10V, Positive-QTOF	splash10-000i-0900000000-adcdc296c2ae6664c9db	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 20V, Positive-QTOF	splash10-00du-0900000000-9836c3795877cca47250	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 40V, Positive-QTOF	splash10-002f-2900000000-22946ed9f61bbf1d579c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 10V, Negative-QTOF	splash10-000i-0900000000-7005f1ac861ec3089be3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 20V, Negative-QTOF	splash10-0a4i-0900000000-31429a57fc38aad65f0d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 40V, Negative-QTOF	splash10-056r-9800000000-8220dd2b30b2d3f39002	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 10V, Negative-QTOF	splash10-000i-0900000000-2f96e00f159950cb03b8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 20V, Negative-QTOF	splash10-0udi-0900000000-fdf6ef885f74b3fa83a8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 40V, Negative-QTOF	splash10-0udi-0900000000-f9cb3cf4e2f5d4eee651	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 10V, Positive-QTOF	splash10-000i-0900000000-e09d74d6ab225fbeff54	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 20V, Positive-QTOF	splash10-000i-0900000000-473628e7743cde5d31ea	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methoxy-1H-indole-3-acetonitrile 40V, Positive-QTOF	splash10-003r-0900000000-e31799a61db96fd930e4	2021-09-22	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]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	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

FDB020828

KNApSAcK ID

C00000105

Chemspider ID

10129174

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11954881

PDB ID

Not Available

ChEBI ID

Not Available

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 1-Methoxy-1H-indole-3-acetonitrile (HMDB0040973)

MOL for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

3D MOL for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

3D SDF for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

3D-SDF for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

PDB for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

3D PDB for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

SMILES for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

INCHI for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

Structure for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

3D Structure for HMDB0040973 (1-Methoxy-1H-indole-3-acetonitrile)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra