NP-MRD: Showing NP-Card for 6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid (NP0219099)

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Record Information

Version

2.0

Created at

2022-09-05 19:59:03 UTC

Updated at

2022-09-05 19:59:03 UTC

NP-MRD ID

NP0219099

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid

Description

6-(D-glucosyloxy)indole-3-carboxylic acid, also known as 6-glco-i3co2h, belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. 6-(D-glucosyloxy)indole-3-carboxylic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. 6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid is found in Arabidopsis thaliana. Based on a literature review very few articles have been published on 6-(D-glucosyloxy)indole-3-carboxylic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052221592D          

 24 26  0  0  1  0            999 V2000
    0.0768   -2.3215    0.0000 O   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
    1.4358   -2.7631    0.0000 O   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
    0.6538   -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
    4.0668    0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957    0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102   -0.2854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.9246    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102   -1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.9246   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -1.5229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4957   -2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 O   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  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  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  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 11 20  1  0  0  0  0
 20 21  1  1  0  0  0
  9 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
  4 24  1  0  0  0  0
  7 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0219099

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1OC(OC2=CC=C3C(NC=C3C(O)=O)=C2)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H17NO8/c17-5-10-11(18)12(19)13(20)15(24-10)23-6-1-2-7-8(14(21)22)4-16-9(7)3-6/h1-4,10-13,15-20H,5H2,(H,21,22)/t10-,11-,12+,13-,15?/m1/s1

> <INCHI_KEY>
KVKJZZMEYYZNDI-CKMVWSRUSA-N

> <FORMULA>
C15H17NO8

> <MOLECULAR_WEIGHT>
339.3

> <EXACT_MASS>
339.095416511

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
32.346737770404026

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H-indole-3-carboxylic acid

> <JCHEM_LOGP>
-0.8420426980000004

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.200126398484782

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.522586543431266

> <JCHEM_PKA_STRONGEST_BASIC>
-2.98109234371272

> <JCHEM_POLAR_SURFACE_AREA>
152.47

> <JCHEM_REFRACTIVITY>
78.52600000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
6-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H-indole-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0       0.143  -4.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.680  -5.158   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.591   0.237   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.925  -0.533   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.259   0.237   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      11.592  -0.533   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.926   0.237   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.926   1.777   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.592  -2.073   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      12.926  -2.843   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.259  -2.843   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.259  -4.383   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.925  -2.073   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.591  -2.843   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   24                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   24                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   22                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   20                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   11   21                                                  
CONECT   21   20                                                            
CONECT   22    9   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23    4    7                                                  
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Value	Source
6-GlcO-I3co2h	ChEBI
6-Glucosyloxyindole-3-carboxylic acid	ChEBI
6-Glucosyloxyindole-3-carboxylate	Generator
6-(D-Glucosyloxy)indole-3-carboxylate	Generator

Chemical Formula

C₁₅H₁₇NO₈

Average Mass

339.3000 Da

Monoisotopic Mass

339.09542 Da

IUPAC Name

6-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H-indole-3-carboxylic acid

Traditional Name

6-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H-indole-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1OC(OC2=CC=C3C(NC=C3C(O)=O)=C2)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C15H17NO8/c17-5-10-11(18)12(19)13(20)15(24-10)23-6-1-2-7-8(14(21)22)4-16-9(7)3-6/h1-4,10-13,15-20H,5H2,(H,21,22)/t10-,11-,12+,13-,15?/m1/s1

InChI Key

KVKJZZMEYYZNDI-CKMVWSRUSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Hexose monosaccharide
Indolecarboxylic acid derivative
O-glycosyl compound
Indole
Indole or derivatives
Pyrrole-3-carboxylic acid
Pyrrole-3-carboxylic acid or derivatives
Benzenoid
Substituted pyrrole
Oxane
Monosaccharide
Vinylogous amide
Pyrrole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Azacycle
Polyol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Carboxylic acid
Alcohol
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

D-glucoside (CHEBI:65025 )
indolyl carbohydrate (CHEBI:65025 )

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	-0.84	ChemAxon
pKa (Strongest Acidic)	3.52	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	152.47 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	78.53 m³·mol⁻¹	ChemAxon
Polarizability	32.35 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

28532791

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70678633

PDB ID

Not Available

ChEBI ID

65025

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid (NP0219099)

MOL for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

3D MOL for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

3D SDF for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

3D-SDF for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

PDB for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

3D PDB for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

SMILES for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

INCHI for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

Structure for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)

3D Structure for NP0219099 (6-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h-indole-3-carboxylic acid)