NP-MRD: Showing NP-Card for (-)-Methyl dioxindole-3-acetate (NP0078016)

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Record Information

Version

2.0

Created at

2022-04-28 23:09:26 UTC

Updated at

2022-04-28 23:09:26 UTC

NP-MRD ID

NP0078016

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Methyl dioxindole-3-acetate

Description

Methyl 2-[(3S)-2,3-dihydroxy-3H-indol-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. (-)-Methyl dioxindole-3-acetate is found in Cephalanceropsis gracilis, Coix lachryma-jobi var. ma-yuen and Coix lacrima-jobi var.ma-yuen. Based on a literature review a small amount of articles have been published on methyl 2-[(3S)-2,3-dihydroxy-3H-indol-3-yl]acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292201092D          

 16 17  0  0  1  0            999 V2000
    3.3523    1.9354    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    0.6979    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
    2.6378    2.3479    0.0000 C   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
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5314    0.2971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3018    0.0468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6829   -0.4988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0990   -0.2357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8460   -1.3075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6279   -1.5707    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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0078016

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@@]1(O)C(=O)NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C11H11NO4/c1-16-9(13)6-11(15)7-4-2-3-5-8(7)12-10(11)14/h2-5,15H,6H2,1H3,(H,12,14)/t11-/m0/s1

> <INCHI_KEY>
BHWUWPHGCCRYBU-NSHDSACASA-N

> <FORMULA>
C11H11NO4

> <MOLECULAR_WEIGHT>
221.212

> <EXACT_MASS>
221.068807838

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.32774161077363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-[(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]acetate

> <ALOGPS_LOGP>
0.29

> <JCHEM_LOGP>
0.29373975833333366

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.678114428485799

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.485208880033573

> <JCHEM_PKA_STRONGEST_BASIC>
-4.273679468845271

> <JCHEM_POLAR_SURFACE_AREA>
75.63000000000001

> <JCHEM_REFRACTIVITY>
56.440900000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(3S)-3-hydroxy-2-oxo-1H-indol-3-yl]acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       6.258   3.613   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       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.320   2.843   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.992   0.555   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.430   0.087   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.275  -0.931   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.185  -0.440   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.579  -2.441   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.039  -2.932   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    4   11   12                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
Methyl 2-[(3S)-2,3-dihydroxy-3H-indol-3-yl]acetic acid	Generator

Chemical Formula

C₁₁H₁₁NO₄

Average Mass

221.2120 Da

Monoisotopic Mass

221.06881 Da

IUPAC Name

methyl 2-[(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]acetate

Traditional Name

methyl [(3S)-3-hydroxy-2-oxo-1H-indol-3-yl]acetate

CAS Registry Number

Not Available

SMILES

COC(=O)C[C@@]1(O)C(=O)NC2=CC=CC=C12

InChI Identifier

InChI=1S/C11H11NO4/c1-16-9(13)6-11(15)7-4-2-3-5-8(7)12-10(11)14/h2-5,15H,6H2,1H3,(H,12,14)/t11-/m0/s1

InChI Key

BHWUWPHGCCRYBU-NSHDSACASA-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
Cephalanceropsis gracilis	-	KNApSAcK
Coix lachryma-jobi var. ma-yuen	Plant	KNApSAcK
Coix lacrima-jobi var.ma-yuen	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
Tertiary alcohol
Methyl ester
Carboxamide group
Carboxylic acid ester
Lactam
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Azacycle
Organonitrogen compound
Carbonyl group
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
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	0.29	ALOGPS
logP	0.29	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	11.49	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.63 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	56.44 m³·mol⁻¹	ChemAxon
Polarizability	21.33 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92449352

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (-)-Methyl dioxindole-3-acetate (NP0078016)

MOL for NP0078016 ((-)-Methyl dioxindole-3-acetate)

3D MOL for NP0078016 ((-)-Methyl dioxindole-3-acetate)

3D SDF for NP0078016 ((-)-Methyl dioxindole-3-acetate)

3D-SDF for NP0078016 ((-)-Methyl dioxindole-3-acetate)

PDB for NP0078016 ((-)-Methyl dioxindole-3-acetate)

3D PDB for NP0078016 ((-)-Methyl dioxindole-3-acetate)

SMILES for NP0078016 ((-)-Methyl dioxindole-3-acetate)

INCHI for NP0078016 ((-)-Methyl dioxindole-3-acetate)

Structure for NP0078016 ((-)-Methyl dioxindole-3-acetate)

3D Structure for NP0078016 ((-)-Methyl dioxindole-3-acetate)