NP-MRD: Showing NP-Card for 6-Hydroxydelphinidin 3-(6-malonylglucoside) (NP0060962)

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Record Information

Version

2.0

Created at

2022-04-28 05:54:42 UTC

Updated at

2022-04-28 05:54:42 UTC

NP-MRD ID

NP0060962

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-Hydroxydelphinidin 3-(6-malonylglucoside)

Description

3-{[(2S,3S,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,6,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position. 6-Hydroxydelphinidin 3-(6-malonylglucoside) is found in Alstroemeria spp. Based on a literature review very few articles have been published on 3-{[(2S,3S,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,6,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282207542D          

 40 43  0  0  1  0            999 V2000
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    0.0000   -3.3000    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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 13 28  1  1  0  0  0
  8 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
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 31 37  1  0  0  0  0
  3 38  1  0  0  0  0
  2 39  1  0  0  0  0
  1 40  1  0  0  0  0
M  CHG  1   7   1
M  END

     RDKit          3D

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 32 34  2  0
 11 35  1  0
 35 36  1  0
 35 37  1  0
 37 38  1  0
 37 39  1  0
 25 13  1  0
 34 26  1  0
 23 15  1  0
 40 63  1  0
 39 62  1  1
  9 46  1  1
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  4 42  1  0
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  3 41  1  0
 11 47  1  6
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 27 53  1  0
 29 54  1  0
 31 55  1  0
 33 56  1  0
 34 57  1  0
 35 58  1  6
 36 59  1  0
 37 60  1  6
 38 61  1  0
M  CHG  1  24   1
M  END


  Mrv1652304282207542D          

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 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 15 26  1  6  0  0  0
 14 27  1  1  0  0  0
 13 28  1  1  0  0  0
  8 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 29 34  1  0  0  0  0
 33 35  1  0  0  0  0
 32 36  1  0  0  0  0
 31 37  1  0  0  0  0
  3 38  1  0  0  0  0
  2 39  1  0  0  0  0
  1 40  1  0  0  0  0
M  CHG  1   7   1
M  END
> <DATABASE_ID>
NP0060962

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](COC(=O)CC(O)=O)O[C@@H](OC2=CC3=C(O)C(O)=C(O)C=C3[O+]=C2C2=CC(O)=C(O)C(O)=C2)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H22O16/c25-9-1-7(2-10(26)18(9)32)23-13(3-8-12(38-23)4-11(27)19(33)17(8)31)39-24-22(36)21(35)20(34)14(40-24)6-37-16(30)5-15(28)29/h1-4,14,20-22,24,34-36H,5-6H2,(H6-,25,26,27,28,29,31,32,33)/p+1/t14-,20-,21+,22+,24-/m1/s1

> <INCHI_KEY>
QXFOCULEMPJHGO-RTLACTJSSA-O

> <FORMULA>
C24H23O16

> <MOLECULAR_WEIGHT>
567.431

> <EXACT_MASS>
567.098061081

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
51.977157611873146

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3S,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,6,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
1.39

> <JCHEM_LOGP>
0.10669999999999957

> <ALOGPS_LOGS>
-2.88

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.606500724372639

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.295483295943247

> <JCHEM_PKA_STRONGEST_BASIC>
-3.954307534548353

> <JCHEM_POLAR_SURFACE_AREA>
277.27

> <JCHEM_REFRACTIVITY>
135.71490000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.98e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3S,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,6,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -8.470   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000  -6.160   0.000  0.00  0.00           O+1
HETATM    8  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.002  -1.540   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.336  -3.850   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      10.669  -1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.337  -1.540   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      12.003  -3.850   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       6.668   0.770   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.334   0.770   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -1.334  -3.850   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.001  -3.850   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -5.335  -1.540   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       5.335  -6.160   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       2.667 -10.780   0.000  0.00  0.00           O+0
CONECT    1    2    6   40                                                  
CONECT    2    1    3   39                                                  
CONECT    3    2    4   38                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   29                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   28                                                  
CONECT   14   13   15   27                                                  
CONECT   15   14   16   26                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   12                                                       
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   15                                                            
CONECT   27   14                                                            
CONECT   28   13                                                            
CONECT   29    8   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   37                                                  
CONECT   32   31   33   36                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33   29                                                       
CONECT   35   33                                                            
CONECT   36   32                                                            
CONECT   37   31                                                            
CONECT   38    3                                                            
CONECT   39    2                                                            
CONECT   40    1                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₃O₁₆

Average Mass

567.4310 Da

Monoisotopic Mass

567.09806 Da

IUPAC Name

3-{[(2S,3S,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,6,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

Traditional Name

3-{[(2S,3S,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,6,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-1lambda4-chromen-1-ylium

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COC(=O)CC(O)=O)O[C@@H](OC2=CC3=C(O)C(O)=C(O)C=C3[O+]=C2C2=CC(O)=C(O)C(O)=C2)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C24H22O16/c25-9-1-7(2-10(26)18(9)32)23-13(3-8-12(38-23)4-11(27)19(33)17(8)31)39-24-22(36)21(35)20(34)14(40-24)6-37-16(30)5-15(28)29/h1-4,14,20-22,24,34-36H,5-6H2,(H6-,25,26,27,28,29,31,32,33)/p+1/t14-,20-,21+,22+,24-/m1/s1

InChI Key

QXFOCULEMPJHGO-RTLACTJSSA-O

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
Alstroemeria spp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Anthocyanidin-3-O-glycosides

Alternative Parents

Substituents

Anthocyanidin-3-o-glycoside
Flavonoid-3-o-glycoside
Hydroxyflavonoid
7-hydroxyflavonoid
6-hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
3'-hydroxyflavonoid
Anthocyanidin
O-glycosyl compound
Glycosyl compound
1-benzopyran
Benzopyran
Pyrogallol derivative
Benzenetriol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
1,3-dicarbonyl compound
Oxane
Monosaccharide
Dicarboxylic acid or derivatives
Monocyclic benzene moiety
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Carboxylic acid
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Organic cation
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	1.39	ALOGPS
logP	0.11	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	3.3	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	277.27 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	135.71 m³·mol⁻¹	ChemAxon
Polarizability	51.98 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

163195485

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 6-Hydroxydelphinidin 3-(6-malonylglucoside) (NP0060962)

MOL for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

3D MOL for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

3D SDF for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

3D-SDF for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

PDB for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

3D PDB for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

SMILES for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

INCHI for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

Structure for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))

3D Structure for NP0060962 (6-Hydroxydelphinidin 3-(6-malonylglucoside))