NP-MRD: Showing NP-Card for 3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium (NP0325417)

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Record Information

Version

2.0

Created at

2022-09-12 06:09:56 UTC

Updated at

2022-09-12 06:09:56 UTC

NP-MRD ID

NP0325417

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Cyanidin 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. Cyanidin 3-(6''-malonylglucoside) is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, cyanidin 3-(6''-malonylglucoside) is found, on average, in the highest concentration in a few different foods, such as rubus (blackberry, raspberry), sweet oranges, and garden onion (var.) And in a lower concentration in lettuces. Cyanidin 3-(6''-malonylglucoside) has also been detected, but not quantified in, several different foods, such as green vegetables, highbush blueberries, garlics, endives, and lupines. 3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium is found in Lactuca sativa. This could make cyanidin 3-(6''-malonylglucoside) a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061310082D          

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M  CHG  1  36   1
M  END

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M  CHG  1  23   1
M  END


  Mrv0541 05061310082D          

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 36 15  2  0  0  0  0
 36 23  1  0  0  0  0
 37 16  1  0  0  0  0
 37 24  1  0  0  0  0
 38 17  1  0  0  0  0
 38 24  1  0  0  0  0
M  CHG  1  36   1
M  END
> <DATABASE_ID>
NP0325417

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(COC(=O)CC(O)=O)OC(OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC(O)=C(O)C=C2)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H22O14/c25-10-4-13(27)11-6-16(23(36-15(11)5-10)9-1-2-12(26)14(28)3-9)37-24-22(34)21(33)20(32)17(38-24)8-35-19(31)7-18(29)30/h1-6,17,20-22,24,32-34H,7-8H2,(H4-,25,26,27,28,29,30)/p+1

> <INCHI_KEY>
ROQLTZUOXIQBDO-UHFFFAOYSA-O

> <FORMULA>
C24H23O14

> <MOLECULAR_WEIGHT>
535.431

> <EXACT_MASS>
535.108780444

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
49.417277321656144

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.82

> <JCHEM_LOGP>
0.6754999999999987

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.388650021940776

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2947491819289443

> <JCHEM_PKA_STRONGEST_BASIC>
-3.649103090718371

> <JCHEM_POLAR_SURFACE_AREA>
236.80999999999995

> <JCHEM_REFRACTIVITY>
131.75309999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.52e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.669   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.668   2.310   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       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -12.003   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -9.336   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0     -13.337   1.540   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0     -12.003   3.850   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -9.336   3.850   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+1
HETATM   37  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1   12                                                       
CONECT    3    9   14                                                       
CONECT    4   10   13                                                       
CONECT    5   10   15                                                       
CONECT    6   11   16                                                       
CONECT    7   18   19                                                       
CONECT    8   17   35                                                       
CONECT    9    1    3   23                                                  
CONECT   10    4    5   25                                                  
CONECT   11    6   13   15                                                  
CONECT   12    2   14   26                                                  
CONECT   13    4   11   27                                                  
CONECT   14    3   12   28                                                  
CONECT   15    5   11   36                                                  
CONECT   16    6   23   37                                                  
CONECT   17    8   20   38                                                  
CONECT   18    7   29   30                                                  
CONECT   19    7   31   35                                                  
CONECT   20   17   21   32                                                  
CONECT   21   20   22   33                                                  
CONECT   22   21   24   34                                                  
CONECT   23    9   16   36                                                  
CONECT   24   22   37   38                                                  
CONECT   25   10                                                            
CONECT   26   12                                                            
CONECT   27   13                                                            
CONECT   28   14                                                            
CONECT   29   18                                                            
CONECT   30   18                                                            
CONECT   31   19                                                            
CONECT   32   20                                                            
CONECT   33   21                                                            
CONECT   34   22                                                            
CONECT   35    8   19                                                       
CONECT   36   15   23                                                       
CONECT   37   16   24                                                       
CONECT   38   17   24                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
Cyanidin 3-(6-malonylglucoside)	HMDB
Cyanidin 3-malonylglucoside	HMDB
Cyanidin 3-O-(6''-malonyl-glucoside)	HMDB

Chemical Formula

C₂₄H₂₃O₁₄

Average Mass

535.4310 Da

Monoisotopic Mass

535.10878 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC1C(COC(=O)CC(O)=O)OC(OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC(O)=C(O)C=C2)C(O)C1O

InChI Identifier

InChI=1S/C24H22O14/c25-10-4-13(27)11-6-16(23(36-15(11)5-10)9-1-2-12(26)14(28)3-9)37-24-22(34)21(33)20(32)17(38-24)8-35-19(31)7-18(29)30/h1-6,17,20-22,24,32-34H,7-8H2,(H4-,25,26,27,28,29,30)/p+1

InChI Key

ROQLTZUOXIQBDO-UHFFFAOYSA-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
Lactuca sativa	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

Not Available

Substituents

Not Available

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	0.82	ALOGPS
logP	0.68	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	3.29	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	236.81 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	131.75 m³·mol⁻¹	ChemAxon
Polarizability	49.42 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

HMDB0037974

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017151

KNApSAcK ID

C00006796

Chemspider ID

8318889

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10143380

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium (NP0325417)

MOL for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

3D MOL for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

3D SDF for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

3D-SDF for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

PDB for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

3D PDB for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

SMILES for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

INCHI for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

Structure for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)

3D Structure for NP0325417 (3-[(6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium)