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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:52:46 UTC

Update Date

2022-03-07 02:53:31 UTC

HMDB ID

HMDB0032937

Secondary Accession Numbers

HMDB32937

Metabolite Identification

Common Name

Methyl 4-chloro-1H-indole-3-acetate

Description

Methyl 4-chloro-1H-indole-3-acetate belongs to the class of organic compounds known as indole-3-acetic acid derivatives. Indole-3-acetic acid derivatives are compounds containing an acetic acid (or a derivative) linked to the C3 carbon atom of an indole. Methyl 4-chloro-1H-indole-3-acetate has been detected, but not quantified in, several different foods, such as broad beans (Vicia faba), common peas (Pisum sativum), grass peas (Lathyrus sativus), lentils (Lens culinaris), and pulses. This could make methyl 4-chloro-1H-indole-3-acetate a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Methyl 4-chloro-1H-indole-3-acetate.

Structure

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


  Mrv0541 05061306482D          

 15 16  0  0  0  0            999 V2000
   -0.9851    4.1027    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
    0.8838    2.9750    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    2.1904    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
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    3.1465    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
    2.6378    3.1729    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752    2.5334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781    3.9312    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
  7  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
 10  5  1  0  0  0  0
 11  7  1  0  0  0  0
 11  8  2  0  0  0  0
 11  9  1  0  0  0  0
 12  8  1  0  0  0  0
 13  6  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  2  0  0  0  0
 15  1  1  0  0  0  0
 15 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032937

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)CC1=CNC2=CC=CC(Cl)=C12

> <INCHI_IDENTIFIER>
InChI=1S/C11H10ClNO2/c1-15-10(14)5-7-6-13-9-4-2-3-8(12)11(7)9/h2-4,6,13H,5H2,1H3

> <INCHI_KEY>
SYPGJEURLIGNPE-UHFFFAOYSA-N

> <FORMULA>
C11H10ClNO2

> <MOLECULAR_WEIGHT>
223.656

> <EXACT_MASS>
223.040006276

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
21.890012081002315

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-(4-chloro-1H-indol-3-yl)acetate

> <ALOGPS_LOGP>
3.26

> <JCHEM_LOGP>
2.459694830666667

> <ALOGPS_LOGS>
-2.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.714733615171085

> <JCHEM_PKA_STRONGEST_BASIC>
-7.0782080280154345

> <JCHEM_POLAR_SURFACE_AREA>
42.09

> <JCHEM_REFRACTIVITY>
58.026

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.83e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 2-(4-chloro-1H-indol-3-yl)acetate

> <JCHEM_VEBER_RULE>
0

$$$$

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      -1.839   7.658   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       1.650   5.553   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.143   5.873   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 Cl   UNK     0       4.924   5.923   0.000  0.00  0.00          Cl+0
HETATM   13  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      -0.887   4.729   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.332   7.338   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2    3    4                                                       
CONECT    3    2    8                                                       
CONECT    4    2    9                                                       
CONECT    5    7   10                                                       
CONECT    6    7   13                                                       
CONECT    7    5    6   11                                                  
CONECT    8    3   11   12                                                  
CONECT    9    4   11   13                                                  
CONECT   10    5   14   15                                                  
CONECT   11    7    8    9                                                  
CONECT   12    8                                                            
CONECT   13    6    9                                                       
CONECT   14   10                                                            
CONECT   15    1   10                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Methyl 4-chloro-1H-indole-3-acetic acid	Generator
4-Chloroindolyl-3-acetic acid methyl ester	MeSH
Methyl 4-chloroindolyl-3-acetate	MeSH
1H-Indole-3-acetic acid, 4-chloro-, methyl ester	HMDB
4-chloro-Indoleacetic acid methyl ester	HMDB
4-Chloroindole-3-acetic acid methyl ester	HMDB
Methyl (4-chloro-1H-indol-3-yl)acetate	HMDB
Methyl 2-(4-chloro-1H-indol-3-yl)acetic acid	Generator

Chemical Formula

C₁₁H₁₀ClNO₂

Average Molecular Weight

223.656

Monoisotopic Molecular Weight

223.040006276

IUPAC Name

methyl 2-(4-chloro-1H-indol-3-yl)acetate

Traditional Name

methyl 2-(4-chloro-1H-indol-3-yl)acetate

CAS Registry Number

19077-78-2

SMILES

COC(=O)CC1=CNC2=CC=CC(Cl)=C12

InChI Identifier

InChI=1S/C11H10ClNO2/c1-15-10(14)5-7-6-13-9-4-2-3-8(12)11(7)9/h2-4,6,13H,5H2,1H3

InChI Key

SYPGJEURLIGNPE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indole-3-acetic acid derivatives. Indole-3-acetic acid derivatives are compounds containing an acetic acid (or a derivative) linked to the C3 carbon atom of an indole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolyl carboxylic acids and derivatives

Direct Parent

Indole-3-acetic acid derivatives

Alternative Parents

Substituents

Indole-3-acetic acid derivative
3-alkylindole
Indole
Aryl chloride
Aryl halide
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Methyl ester
Carboxylic acid ester
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Azacycle
Organochloride
Organohalogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic oxygen 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: HMDB0032937)
Cell membrane (HMDB: HMDB0032937)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0032937)

Source

Exogenous

Exogenous (HMDB: HMDB0032937)

Food

Food (HMDB: HMDB0032937)

Pulse

Lentil

Lentils (FooDB: FOOD00098)

Pea

Common pea (FooDB: FOOD00141)
Grass pea (FooDB: FOOD00096)

Bean

Broad bean (FooDB: FOOD00197)

Pulses (FooDB: FOOD00867)

Endogenous

Plant

Fabaceae (HMDB: HMDB0032937)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0032937)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	120 - 121 °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	0.38 g/L	ALOGPS
logP	3.26	ALOGPS
logP	2.46	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	14.71	ChemAxon
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	42.09 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	58.03 m³·mol⁻¹	ChemAxon
Polarizability	21.89 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	179.042	30932474
DeepCCS	[M+Na]+	154.41	30932474
AllCCS	[M+H]+	146.5	32859911
AllCCS	[M+H-H2O]+	142.5	32859911
AllCCS	[M+NH4]+	150.3	32859911
AllCCS	[M+Na]+	151.4	32859911
AllCCS	[M-H]-	146.4	32859911
AllCCS	[M+Na-2H]-	146.5	32859911
AllCCS	[M+HCOO]-	146.7	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.	6.94 minutes	32390414
Predicted by Siyang on May 30, 2022	15.3017 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.1 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2387.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	524.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	177.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	335.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	348.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	636.0 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	642.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	152.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1305.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	495.1 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	1470.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	513.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	413.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	404.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	350.8 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	18.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methyl 4-chloro-1H-indole-3-acetate	COC(=O)CC1=CNC2=CC=CC(Cl)=C12	2703.8	Standard polar	33892256
Methyl 4-chloro-1H-indole-3-acetate	COC(=O)CC1=CNC2=CC=CC(Cl)=C12	1826.6	Standard non polar	33892256
Methyl 4-chloro-1H-indole-3-acetate	COC(=O)CC1=CNC2=CC=CC(Cl)=C12	2069.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Methyl 4-chloro-1H-indole-3-acetate,1TMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C)C2=CC=CC(Cl)=C12	2029.8	Semi standard non polar	33892256
Methyl 4-chloro-1H-indole-3-acetate,1TMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C)C2=CC=CC(Cl)=C12	1954.0	Standard non polar	33892256
Methyl 4-chloro-1H-indole-3-acetate,1TBDMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC(Cl)=C12	2245.1	Semi standard non polar	33892256
Methyl 4-chloro-1H-indole-3-acetate,1TBDMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC(Cl)=C12	2153.6	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-1910000000-4307e16409e3256c6ae4	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-03xr-9810000000-6ffaf0a6ebdf9ae51f7f	2015-03-01	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 10V, Positive-QTOF	splash10-00dl-0960000000-a56bcbf939c1a10a909d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 20V, Positive-QTOF	splash10-0w93-0920000000-c28486054114a2071e46	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 40V, Positive-QTOF	splash10-03di-1900000000-e05d39259ff12b423ab7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 10V, Negative-QTOF	splash10-00di-0490000000-55af41b7d3689f428150	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 20V, Negative-QTOF	splash10-00dl-1980000000-85fdc5730f7cf3bc53c3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 40V, Negative-QTOF	splash10-0f6x-2900000000-feaab463a70ed99756cb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 10V, Positive-QTOF	splash10-0229-0790000000-58dc2a0d0ad232ca6587	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 20V, Positive-QTOF	splash10-01vo-0930000000-c45904daa4bc84ec17ee	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 40V, Positive-QTOF	splash10-01ti-0900000000-9138b3f910fe978a7a6d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 10V, Negative-QTOF	splash10-00dl-0980000000-932b44efd1dacb0615d0	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 20V, Negative-QTOF	splash10-001i-9400000000-fa410ada426e20a2fdce	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 4-chloro-1H-indole-3-acetate 40V, Negative-QTOF	splash10-03e9-3900000000-797293c7299d14957314	2021-09-24	Wishart 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

FDB010922

KNApSAcK ID

C00000103

Chemspider ID

141665

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

161268

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 Methyl 4-chloro-1H-indole-3-acetate (HMDB0032937)

MOL for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

3D MOL for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

3D SDF for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

3D-SDF for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

PDB for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

3D PDB for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

SMILES for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

INCHI for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

Structure for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

3D Structure for HMDB0032937 (Methyl 4-chloro-1H-indole-3-acetate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra