NP-MRD: Showing NP-Card for 3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium (NP0171824)

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Record Information

Version

2.0

Created at

2022-09-03 08:30:10 UTC

Updated at

2022-09-03 08:30:10 UTC

NP-MRD ID

NP0171824

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium

Description

Pelargonidin 3-(6''-malonylglucoside) 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. 3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium is found in Callistephus chinensis. Based on a literature review a small amount of articles have been published on Pelargonidin 3-(6''-malonylglucoside).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032210302D          

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M  CHG  1  23   1
M  END

     RDKit          3D

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M  CHG  1  23   1
M  END


  Mrv1652309032210302D          

 37 40  0  0  1  0            999 V2000
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M  CHG  1  23   1
M  END
> <DATABASE_ID>
NP0171824

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1C(COC(=O)CC(O)=O)O[C@@H](OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC=C(O)C=C2)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H22O13/c25-11-3-1-10(2-4-11)23-16(7-13-14(27)5-12(26)6-15(13)35-23)36-24-22(33)21(32)20(31)17(37-24)9-34-19(30)8-18(28)29/h1-7,17,20-22,24,31-33H,8-9H2,(H3-,25,26,27,28,29)/p+1/t17?,20-,21?,22?,24-/m1/s1

> <INCHI_KEY>
XLZUBCUKXQFBKB-GRAUSCIISA-O

> <FORMULA>
C24H23O13

> <MOLECULAR_WEIGHT>
519.434

> <EXACT_MASS>
519.113317221

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
48.54614204822843

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.87

> <JCHEM_LOGP>
0.9598999999999989

> <ALOGPS_LOGS>
-3.25

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.397137470862175

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2955237885215536

> <JCHEM_PKA_STRONGEST_BASIC>
-3.64910309071837

> <JCHEM_POLAR_SURFACE_AREA>
216.57999999999998

> <JCHEM_REFRACTIVITY>
129.77220000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.10e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  O   UNK     0      -4.001 -13.090   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.667 -13.860   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667 -15.400   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.334 -13.090   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000 -13.860   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000 -15.400   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.334 -13.090   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667 -13.860   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001 -13.090   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335 -13.860   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.668 -13.090   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.002 -13.860   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.336 -13.090   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.669 -10.780   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.336  -8.470   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      12.003  -8.470   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      14.670  -8.470   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      13.337 -10.780   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.003 -11.550   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      12.003 -13.090   0.000  0.00  0.00           O+1
HETATM   24  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.669 -15.400   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.003 -16.170   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.003 -17.710   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.669 -18.480   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.669 -20.020   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       9.336 -17.710   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.002 -10.780   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.335 -10.780   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.667 -10.780   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   36                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   32                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   24                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   15   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   13   25                                                  
CONECT   25   24   26   31                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   25                                                       
CONECT   32   11   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34    9   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₃O₁₃

Average Mass

519.4340 Da

Monoisotopic Mass

519.11332 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

O[C@@H]1C(COC(=O)CC(O)=O)O[C@@H](OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC=C(O)C=C2)C(O)C1O

InChI Identifier

InChI=1S/C24H22O13/c25-11-3-1-10(2-4-11)23-16(7-13-14(27)5-12(26)6-15(13)35-23)36-24-22(33)21(32)20(31)17(37-24)9-34-19(30)8-18(28)29/h1-7,17,20-22,24,31-33H,8-9H2,(H3-,25,26,27,28,29)/p+1/t17?,20-,21?,22?,24-/m1/s1

InChI Key

XLZUBCUKXQFBKB-GRAUSCIISA-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, 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
Callistephus chinensis	LOTUS Database	35616633

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
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Anthocyanidin
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
1,3-dicarbonyl compound
Dicarboxylic acid or derivatives
Monosaccharide
Benzenoid
Oxane
Heteroaromatic compound
Carboxylic acid ester
Secondary alcohol
Oxacycle
Acetal
Carboxylic acid derivative
Organoheterocyclic compound
Carboxylic acid
Polyol
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Anthocyanidins (LMPK12010030 )

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00006755

Chemspider ID

24842077

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44256635

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium (NP0171824)

MOL for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D MOL for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D SDF for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D-SDF for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

PDB for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D PDB for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

SMILES for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

INCHI for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

Structure for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)

3D Structure for NP0171824 (3-{[(2s,5s)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1λ⁴-chromen-1-ylium)