NP-MRD: Showing NP-Card for 3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one (NP0307642)

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Record Information

Version

2.0

Created at

2022-09-11 00:54:50 UTC

Updated at

2022-09-11 00:54:50 UTC

NP-MRD ID

NP0307642

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one

Description

3,4-Dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxy-1H-indol-3-yl)methyl]oxolan-2-one belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. 3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one is found in Eutrema salsugineum. 3,4-Dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxy-1H-indol-3-yl)methyl]oxolan-2-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004261512342D          

 35 38  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1533004261512342D          

 35 38  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0307642

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CON1C=C(CC2(O)C(O)C(OC2=O)C(CO)OC2OC(CO)C(O)C(O)C2O)C2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C22H29NO12/c1-32-23-7-10(11-4-2-3-5-12(11)23)6-22(31)19(29)18(35-21(22)30)14(9-25)34-20-17(28)16(27)15(26)13(8-24)33-20/h2-5,7,13-20,24-29,31H,6,8-9H2,1H3

> <INCHI_KEY>
MVJFBVCVQFCINF-UHFFFAOYSA-N

> <FORMULA>
C22H29NO12

> <MOLECULAR_WEIGHT>
499.469

> <EXACT_MASS>
499.168975378

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
48.82606713332079

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxy-1H-indol-3-yl)methyl]oxolan-2-one

> <ALOGPS_LOGP>
-1.24

> <JCHEM_LOGP>
-2.6225989070000004

> <ALOGPS_LOGS>
-1.65

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.22429142635366

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.182635040162515

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835639081477

> <JCHEM_POLAR_SURFACE_AREA>
200.53

> <JCHEM_REFRACTIVITY>
115.26850000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.11e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650   1.408   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.143   1.728   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.018   0.196   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.619   3.192   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.084   3.668   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.627   4.098   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.873   3.192   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.397   1.728   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.302   0.482   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.627   5.638   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.960   6.408   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.960   7.948   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.707   6.408   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.707   7.948   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.627   8.718   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.627  10.258   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.960  11.028   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.960  12.568   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       0.707  11.028   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.707  12.568   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.041  10.258   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       3.374  11.028   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.041   8.718   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       3.374   7.948   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   30                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9   13                                             
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13                                                            
CONECT   15   11   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20   28                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   19   29                                                  
CONECT   29   28                                                            
CONECT   30    5   31   35                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34    3   30                                                  
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₂₉NO₁₂

Average Mass

499.4690 Da

Monoisotopic Mass

499.16898 Da

IUPAC Name

3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxy-1H-indol-3-yl)methyl]oxolan-2-one

Traditional Name

3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one

CAS Registry Number

Not Available

SMILES

CON1C=C(CC2(O)C(O)C(OC2=O)C(CO)OC2OC(CO)C(O)C(O)C2O)C2=CC=CC=C12

InChI Identifier

InChI=1S/C22H29NO12/c1-32-23-7-10(11-4-2-3-5-12(11)23)6-22(31)19(29)18(35-21(22)30)14(9-25)34-20-17(28)16(27)15(26)13(8-24)33-20/h2-5,7,13-20,24-29,31H,6,8-9H2,1H3

InChI Key

MVJFBVCVQFCINF-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, 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
Thellungiella salsuginea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Disaccharide
O-glycosyl compound
3-alkylindole
Indole
Indole or derivatives
Gamma butyrolactone
Benzenoid
Substituted pyrrole
Oxane
Heteroaromatic compound
Tetrahydrofuran
Tertiary alcohol
Pyrrole
Carboxylic acid ester
Lactone
Secondary alcohol
Acetal
Carboxylic acid derivative
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Organic nitrogen compound
Organonitrogen compound
Primary alcohol
Organopnictogen 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	-1.2	ALOGPS
logP	-2.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	11.18	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	200.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	115.27 m³·mol⁻¹	ChemAxon
Polarizability	48.83 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one (NP0307642)

MOL for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

3D MOL for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

3D SDF for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

3D-SDF for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

PDB for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

3D PDB for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

SMILES for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

INCHI for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

Structure for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)

3D Structure for NP0307642 (3,4-dihydroxy-5-(2-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl)-3-[(1-methoxyindol-3-yl)methyl]oxolan-2-one)