NP-MRD: Showing NP-Card for 2,3-Dihydro-2-oxo-1H-indole-3-acetic acid (NP0085007)

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Record Information

Version

1.0

Created at

2022-04-29 05:35:47 UTC

Updated at

2022-04-29 05:35:47 UTC

NP-MRD ID

NP0085007

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3-Dihydro-2-oxo-1H-indole-3-acetic acid

Description

Xi-2,3-Dihydro-2-oxo-1H-indole-3-acetic acid, also known as oxindole-3-acetic acid or 2-oxindol-3-yl-acetate, belongs to the class of organic compounds known as indolyl carboxylic acids and derivatives. Indolyl carboxylic acids and derivatives are compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an indole ring. Xi-2,3-Dihydro-2-oxo-1H-indole-3-acetic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, xi-2,3-Dihydro-2-oxo-1H-indole-3-acetic acid has been detected, but not quantified in, several different foods, such as brassicas, cereals and cereal products, fats and oils, and fruits. 2,3-Dihydro-2-oxo-1H-indole-3-acetic acid is found in Arabidopsis thaliana, Brassica spp., Helianthus annuus , Pinus sylvestris, Ribes rubrum , Solanum lycopersicum, Zea mays and Zea mays . It was first documented in 1984 (PMID: 11540902). This could make XI-2,3-dihydro-2-oxo-1H-indole-3-acetic acid a potential biomarker for the consumption of these foods (PMID: 11538238) (PMID: 11539687) (PMID: 12105962) (PMID: 14519969).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305171800302D          

 14 15  0  0  0  0            999 V2000
   -0.1712   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    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
    2.6378   -1.5229    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
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  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
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 10  2  1  0  0  0  0
  9  4  1  0  0  0  0
 14 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0085007

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CC1C(O)=NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C10H9NO3/c12-9(13)5-7-6-3-1-2-4-8(6)11-10(7)14/h1-4,7H,5H2,(H,11,14)(H,12,13)

> <INCHI_KEY>
ILGMGHZPXRDCCS-UHFFFAOYSA-N

> <FORMULA>
C10H9NO3

> <MOLECULAR_WEIGHT>
191.1834

> <EXACT_MASS>
191.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.767883193047002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(2-hydroxy-3H-indol-3-yl)acetic acid

> <ALOGPS_LOGP>
0.43

> <JCHEM_LOGP>
1.4668200356666665

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.7541057142843

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7374778267910145

> <JCHEM_PKA_STRONGEST_BASIC>
0.8313455880067988

> <JCHEM_POLAR_SURFACE_AREA>
69.89

> <JCHEM_REFRACTIVITY>
51.1809

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.58e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2-hydroxy-3H-indol-3-yl)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  O   UNK     0      -0.320  -1.303   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924  -2.843   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       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.333  -5.798   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -0.887  -3.189   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10    4                                                  
CONECT   10    9   11    2                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol

Synonyms

Value	Source
2-Oxindol-3-yl-acetic acid	ChEBI
Oxindole-3-acetic acid	ChEBI
2-Oxindol-3-yl-acetate	Generator
Oxindole-3-acetate	Generator
XI-2,3-dihydro-2-oxo-1H-indole-3-acetate	Generator
2-(2-oxo-3-Indolinyl)acetic acid	HMDB
2-Hydroxy-1H-indole-3-acetic acid	HMDB
2-Oxindole-3-acetate	Generator
2-Oxindole-3-acetic acid	MeSH

Chemical Formula

C₁₀H₉NO₃

Average Mass

191.1834 Da

Monoisotopic Mass

191.05824 Da

IUPAC Name

2-(2-hydroxy-3H-indol-3-yl)acetic acid

Traditional Name

(2-hydroxy-3H-indol-3-yl)acetic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC1C(O)=NC2=CC=CC=C12

InChI Identifier

InChI=1S/C10H9NO3/c12-9(13)5-7-6-3-1-2-4-8(6)11-10(7)14/h1-4,7H,5H2,(H,11,14)(H,12,13)

InChI Key

ILGMGHZPXRDCCS-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	LOTUS Database	35616633
Brassica spp.	Plant	KNApSAcK
Helianthus annuus L.	Plant	KNApSAcK
Pinus sylvestris	LOTUS Database	35616633
Ribes rubrum	Plant	KNApSAcK
Solanum lycopersicum	LOTUS Database	35616633
Zea mays	LOTUS Database	35616633
Zea mays L.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolyl carboxylic acids and derivatives. Indolyl carboxylic acids and derivatives are compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an indole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolyl carboxylic acids and derivatives

Direct Parent

Indolyl carboxylic acids and derivatives

Alternative Parents

Substituents

Indolyl carboxylic acid derivative
Indole
Dihydroindole
Benzenoid
Carboxamide group
Secondary carboxylic acid amide
Lactam
Carboxylic acid derivative
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Carbonyl group
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	0.43	ALOGPS
logP	1.47	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	3.74	ChemAxon
pKa (Strongest Basic)	0.83	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	69.89 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	51.18 m³·mol⁻¹	ChemAxon
Polarizability	18.77 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

External Links

HMDB ID

HMDB0035514

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014206

KNApSAcK ID

Not Available

Chemspider ID

2338343

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3080590

PDB ID

Not Available

ChEBI ID

133221

Good Scents ID

Not Available

References

General References

Reinecke DM, Bandurski RS: Oxidation of indole-3-acetic acid to oxindole-3-acetic acid by an enzyme preparation from Zea mays. Plant Physiol. 1988;86:868-72. doi: 10.1104/pp.86.3.868. [PubMed:11538238 ]
Nonhebel HM: Measurement of the rates of oxindole-3-acetic acid turnover, and indole-3-acetic acid oxidation in Zea mays seedlings. J Exp Bot. 1986 Nov;37(184):1691-7. doi: 10.1093/jxb/37.11.1691. [PubMed:11539687 ]
Nonhebel HM, Bandurski RS: Oxidation of indole-3-acetic acid and oxindole-3-acetic acid to 2,3-dihydro-7-hydroxy-2-oxo-1H indole-3-acetic acid-7'-O-beta-D-glucopyranoside in Zea mays seedlings. Plant Physiol. 1984;76:979-83. doi: 10.1104/pp.76.4.979. [PubMed:11540902 ]
Hoenicke K, Borchert O, Gruning K, Simat TJ: "Untypical aging off-flavor" in wine: synthesis of potential degradation compounds of indole-3-acetic acid and kynurenine and their evaluation as precursors of 2-aminoacetophenone. J Agric Food Chem. 2002 Jul 17;50(15):4303-9. doi: 10.1021/jf011672r. [PubMed:12105962 ]
Niwa T, Ishii S, Hiramatsu A, Osawa T: Oxidative reaction of oxindole-3-acetic acids. Biosci Biotechnol Biochem. 2003 Sep;67(9):1870-4. doi: 10.1271/bbb.67.1870. [PubMed:14519969 ]

Showing NP-Card for 2,3-Dihydro-2-oxo-1H-indole-3-acetic acid (NP0085007)

MOL for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

3D MOL for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

3D SDF for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

3D-SDF for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

PDB for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

3D PDB for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

SMILES for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

INCHI for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

Structure for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)

3D Structure for NP0085007 (2,3-Dihydro-2-oxo-1H-indole-3-acetic acid)