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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2012-09-11 17:32:20 UTC

Update Date

2023-02-21 17:19:11 UTC

HMDB ID

HMDB0029738

Secondary Accession Numbers

HMDB29738

Metabolite Identification

Common Name

Indole-3-methyl acetate

Description

Indole-3-methyl acetate, also known as methyl indole-3-acetate (methyl-IAA), is a catabolite of tryptophan converted by the gut microbiota. After absorption through the intestinal epithelium, tryptophan catabolites enter the bloodstream and are later excreted in the urine (PMID: 30120222 ). Pediatric enthesitis-related arthritis (ERA) patients (i.e. spondyloarthropathy associated with inflammatory bowel disease) have intestinal inflammation and decreased gut microbial diversity. Such alterations in the gut microbiota resulted in the reduction of tryptophan metabolism and several tryptophan metabolites in pediatric ERA fecal samples, including indole-3-methyl acetate (PMID: 27786174 ). Indole-3-methyl acetate is found in apple, and has been isolated from immature seeds of beach pea (Lathyrus maritimus), Vicia amurensis, wild soybean (Glycine soja), lobiya (Vigna catiang var. sinensis) and hyacinth bean (Dolichos lablab).

Structure

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


  Mrv1652301282019172D          

 14 15  0  0  0  0            999 V2000
 9997.0764 9999.4249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8215 9998.6402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.3735 9998.0272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.1805 9998.1986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.295810000.3109    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8834 9999.5964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4354 9998.9833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.1891 9999.3189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.102810000.1393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9036 9998.9064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.6180 9999.3189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3324 9998.9064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.617910000.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.0469 9999.3189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  9  1  0  0  0  0
  8 10  1  0  0  0  0
  4  7  1  0  0  0  0
  6  1  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 14  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029738

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)CC1=CNC2=C1C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C11H11NO2/c1-14-11(13)6-8-7-12-10-5-3-2-4-9(8)10/h2-5,7,12H,6H2,1H3

> <INCHI_KEY>
KTHADMDGDNYQRX-UHFFFAOYSA-N

> <FORMULA>
C11H11NO2

> <MOLECULAR_WEIGHT>
189.2105

> <EXACT_MASS>
189.078978601

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
19.777863703154345

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.61

> <JCHEM_LOGP>
1.8556501543333335

> <ALOGPS_LOGS>
-2.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.044118914611719

> <JCHEM_PKA_STRONGEST_BASIC>
-7.0781988457999905

> <JCHEM_POLAR_SURFACE_AREA>
42.09

> <JCHEM_REFRACTIVITY>
53.2212

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.15e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 1H-indol-3-ylacetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-JAN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-JAN-20         0                                  
HETATM    1  C   UNK     0    8661.2098665.593   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8660.7338664.128   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8661.7648662.984   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8663.2708663.304   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0    8663.4858667.247   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0    8662.7168665.913   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8663.7468664.769   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8665.1538665.395   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8664.9928666.927   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8666.4878664.625   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8667.8208665.395   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8669.1548664.625   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8667.8208666.935   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8670.4888665.395   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    7                                                       
CONECT    5    6    9                                                       
CONECT    6    7    5    1                                                  
CONECT    7    6    8    4                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    5                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11   14                                                       
CONECT   13   11                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
beta-Indolylacetic acid methyl ester	ChEBI
Indole-3-acetic acid, methyl ester	ChEBI
Methyl 3-indolylacetate	ChEBI
Methyl beta-indoleacetate	ChEBI
Methyl beta-indolylacetate	ChEBI
Methyl indol-3-ylacetate	ChEBI
b-Indolylacetate methyl ester	Generator
b-Indolylacetic acid methyl ester	Generator
beta-Indolylacetate methyl ester	Generator
Β-indolylacetate methyl ester	Generator
Β-indolylacetic acid methyl ester	Generator
Indole-3-acetate, methyl ester	Generator
Methyl 3-indolylacetic acid	Generator
Methyl b-indoleacetate	Generator
Methyl b-indoleacetic acid	Generator
Methyl beta-indoleacetic acid	Generator
Methyl β-indoleacetate	Generator
Methyl β-indoleacetic acid	Generator
Methyl b-indolylacetate	Generator
Methyl b-indolylacetic acid	Generator
Methyl beta-indolylacetic acid	Generator
Methyl β-indolylacetate	Generator
Methyl β-indolylacetic acid	Generator
Methyl indol-3-ylacetic acid	Generator
Indole-3-methyl acetic acid	Generator
1H-Indole-3-acetic acid, methyl ester	HMDB
beta -Indolylacetic acid methyl ester	HMDB
IAA methyl ester	HMDB
Indole-3-acetic acid methyl ester	HMDB
INDOLE-3-acetIC ACID methylester	HMDB
Meiaa	HMDB
Methyl 1H-indol-3-ylacetate	HMDB
Methyl 2-(1H-indol-3-yl)acetate	HMDB
Methyl beta -indoleacetate	HMDB
Methyl beta -indolylacetate	HMDB
Methyl iaa	HMDB
Methyl indole-3-acetate	HMDB
Methylester OF 3-indoleacetic acid	HMDB
Methyl (indol-3-yl)acetic acid	Generator
(1H-Indol-3-yl)acetic acid methyl ester	HMDB
Indolyl-3-acetic acid methyl ester	HMDB
Methyl 1H-indole-3-acetate	HMDB
Methyl-IAA	HMDB

Chemical Formula

C₁₁H₁₁NO₂

Average Molecular Weight

189.2105

Monoisotopic Molecular Weight

189.078978601

IUPAC Name

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

Traditional Name

methyl 1H-indol-3-ylacetate

CAS Registry Number

1912-33-0

SMILES

COC(=O)CC1=CNC2=C1C=CC=C2

InChI Identifier

InChI=1S/C11H11NO2/c1-14-11(13)6-8-7-12-10-5-3-2-4-9(8)10/h2-5,7,12H,6H2,1H3

InChI Key

KTHADMDGDNYQRX-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
Substituted pyrrole
Benzenoid
Heteroaromatic compound
Methyl ester
Pyrrole
Carboxylic acid ester
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Carbonyl group
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

indoles (CHEBI:72782 )
methyl ester (CHEBI:72782 )
a plant hormone (CPD-10546 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 26283345)

Cellular substructure

Membrane (HMDB: HMDB0029738)
Cell membrane (HMDB: HMDB0029738)

Excreta

Biofluid or Excreta

Feces (PMID: 27786174)
Urine (PMID: 28916042)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029738)

Source

Endogenous

Endogenous (HMDB: HMDB0029738)

Plant

Microbe

Clostridium sporogenes (HMDB: HMDB0029738)

Exogenous

Food

Food (HMDB: HMDB0029738)

Fruit

Pome

Apple (FooDB: FOOD00105)

Citrus

Sweet orange (FooDB: FOOD00057)

Drupe

European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)

Berry

Common grape (FooDB: FOOD00204)

Tropical fruit

Japanese persimmon (FooDB: FOOD00073)

Pulse

Bean

Pea

Common pea (FooDB: FOOD00141)

Pulses (FooDB: FOOD00867)

Vegetable

Cabbage

Cauliflower (FooDB: FOOD00031)

Root vegetable

Radish (FooDB: FOOD00153)

Fruit vegetable

Garden tomato (var.) (FooDB: FOOD00173)

Cereal and cereal product

Cereal

Corn (FooDB: FOOD00205)

Nut

Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)

Exogenous (HMDB: HMDB0029738)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	125 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	138.7	http://allccs.zhulab.cn/database/detail?ID=AllCCS00002172

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.15 g/L	ALOGPS
logP	2.61	ALOGPS
logP	1.86	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	15.04	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	53.22 m³·mol⁻¹	ChemAxon
Polarizability	19.78 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
DarkChem	[M+H]+	145.205	31661259
DarkChem	[M-H]-	142.743	31661259
DeepCCS	[M+H]+	139.764	30932474
DeepCCS	[M-H]-	136.888	30932474
DeepCCS	[M-2H]-	173.182	30932474
DeepCCS	[M+Na]+	148.72	30932474
AllCCS	[M+H]+	141.0	32859911
AllCCS	[M+H-H2O]+	136.7	32859911
AllCCS	[M+NH4]+	145.0	32859911
AllCCS	[M+Na]+	146.2	32859911
AllCCS	[M-H]-	143.0	32859911
AllCCS	[M+Na-2H]-	143.2	32859911
AllCCS	[M+HCOO]-	143.6	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.	5.69 minutes	32390414
Predicted by Siyang on May 30, 2022	12.8762 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.48 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2076.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	429.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	152.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	244.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	267.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	490.1 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	478.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	124.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1090.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	425.9 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	1282.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	392.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	361.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	365.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	383.3 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	65.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Indole-3-methyl acetate	COC(=O)CC1=CNC2=C1C=CC=C2	2824.9	Standard polar	33892256
Indole-3-methyl acetate	COC(=O)CC1=CNC2=C1C=CC=C2	1551.9	Standard non polar	33892256
Indole-3-methyl acetate	COC(=O)CC1=CNC2=C1C=CC=C2	1871.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Indole-3-methyl acetate,1TMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C)C2=CC=CC=C12	1851.7	Semi standard non polar	33892256
Indole-3-methyl acetate,1TMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C)C2=CC=CC=C12	1826.0	Standard non polar	33892256
Indole-3-methyl acetate,1TBDMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C12	2073.5	Semi standard non polar	33892256
Indole-3-methyl acetate,1TBDMS,isomer #1	COC(=O)CC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C12	2036.6	Standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	26283345	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Normal	27786174	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Enthesitis-related arthritis	27786174	details
Urine	Detected and Quantified	0.768 umol/mmol creatinine	Adult (>18 years old)	Female	Pregnancy	28916042	details

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

FDB000936

KNApSAcK ID

C00000101

Chemspider ID

67279

KEGG Compound ID

Not Available

BioCyc ID

CPD-10546

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

74706

PDB ID

Not Available

ChEBI ID

72782

Food Biomarker Ontology

Not Available

VMH ID

CE2122

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Stoll ML, Kumar R, Lefkowitz EJ, Cron RQ, Morrow CD, Barnes S: Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors. Genes Immun. 2016 Dec;17(7):400-405. doi: 10.1038/gene.2016.38. Epub 2016 Oct 27. [PubMed:27786174 ]
Roager HM, Licht TR: Microbial tryptophan catabolites in health and disease. Nat Commun. 2018 Aug 17;9(1):3294. doi: 10.1038/s41467-018-05470-4. [PubMed:30120222 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Indole-3-methyl acetate (HMDB0029738)

MOL for HMDB0029738 (Indole-3-methyl acetate)

3D MOL for HMDB0029738 (Indole-3-methyl acetate)

3D SDF for HMDB0029738 (Indole-3-methyl acetate)

3D-SDF for HMDB0029738 (Indole-3-methyl acetate)

PDB for HMDB0029738 (Indole-3-methyl acetate)

3D PDB for HMDB0029738 (Indole-3-methyl acetate)

SMILES for HMDB0029738 (Indole-3-methyl acetate)

INCHI for HMDB0029738 (Indole-3-methyl acetate)

Structure for HMDB0029738 (Indole-3-methyl acetate)

3D Structure for HMDB0029738 (Indole-3-methyl acetate)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized