Showing NP-Card for Cyanidin 3-(malonylsophoroside) 5-glucoside (NP0048965)

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Record Information
Version2.0
Created at2022-03-17 21:04:58 UTC
Updated at2022-03-17 21:04:58 UTC
NP-MRD IDNP0048965
Secondary Accession NumbersNone
Natural Product Identification
Common NameCyanidin 3-(malonylsophoroside) 5-glucoside
DescriptionCyanidin 3-(malonylsophoroside) 5-glucoside belongs to the class of organic compounds known as anthocyanidin-5-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C5-position. Cyanidin 3-(malonylsophoroside) 5-glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, cyanidin 3-(malonylsophoroside) 5-glucoside has been detected, but not quantified in, brassicas and cauliflowers. Cyanidin 3-(malonylsophoroside) 5-glucoside is found in Brassica oleracea . This could make cyanidin 3-(malonylsophoroside) 5-glucoside a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)

  Mrv0541 02241221032D          

 60 65  0  0  0  0            999 V2000
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M  CHG  1   7   1
M  END
Download

3D MOL for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)

Download
3D SDF for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)
  Mrv0541 02241221032D          

 60 65  0  0  0  0            999 V2000
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M  CHG  1   7   1
M  END
> <DATABASE_ID>
NP0048965

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](COC(=O)CC(O)=O)O[C@H]2OC2=CC3=C(C=C(O)C=C3O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C36H42O24/c37-8-19-24(45)27(48)30(51)34(57-19)55-17-5-12(39)4-16-13(17)6-18(32(54-16)11-1-2-14(40)15(41)3-11)56-36-33(60-35-31(52)28(49)25(46)20(9-38)58-35)29(50)26(47)21(59-36)10-53-23(44)7-22(42)43/h1-6,19-21,24-31,33-38,45-52H,7-10H2,(H3-,39,40,41,42,43)/p+1/t19-,20-,21-,24-,25-,26-,27+,28+,29+,30-,31-,33-,34-,35+,36-/m1/s1

> <INCHI_KEY>
ASCBTZBIOSPIRQ-DTYOCLMRSA-O

> <FORMULA>
C36H43O24

> <MOLECULAR_WEIGHT>
859.7122

> <EXACT_MASS>
859.214427304

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
80.00553971725

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-4,5-dihydroxy-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium

> <ALOGPS_LOGP>
-0.22

> <JCHEM_LOGP>
-4.104500000000002

> <ALOGPS_LOGS>
-2.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.648373543726639

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2924599502347482

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6789468869085615

> <JCHEM_POLAR_SURFACE_AREA>
395.11000000000007

> <JCHEM_REFRACTIVITY>
196.31080000000009

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.90e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-4,5-dihydroxy-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)
Download
PDB for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.365  -1.155   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.699  -1.925   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.699  -3.465   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.365  -4.235   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.031  -3.465   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.031  -1.925   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.302  -1.155   0.000  0.00  0.00           O+1
HETATM    8  C   UNK     0       0.302  -4.235   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.636  -3.465   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.636  -1.925   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.970  -1.155   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.303   1.155   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.970   0.385   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.303  -1.925   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.637  -1.155   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.637   0.385   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.303   2.695   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.971   1.155   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -5.032  -1.155   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -5.032  -5.775   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -6.366  -6.545   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.366  -8.085   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.032  -8.855   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.699  -8.085   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.699  -6.545   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -2.365  -5.775   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -2.365  -8.855   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -5.032 -10.395   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -7.700  -8.855   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -7.700  -5.775   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -9.033  -6.545   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       7.947  -7.109   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       9.487  -7.109   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      10.257  -5.775   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       9.487  -4.441   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.947  -4.441   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       7.177  -5.775   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       7.177  -3.108   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      10.257  -3.108   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      11.797  -5.775   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      10.257  -8.442   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      11.797  -8.442   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       1.636  -6.545   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       1.636  -8.085   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       2.970  -8.855   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       4.303  -8.085   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       4.303  -6.545   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       2.970  -5.775   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       2.970  -4.235   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       5.637  -5.775   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       5.637  -8.855   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       2.970 -10.395   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       0.302  -8.855   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0       0.302 -15.730   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0       1.072 -14.396   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0       2.612 -14.396   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0       0.302 -13.062   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       1.072 -11.729   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0       0.302 -10.395   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       2.612 -11.729   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   26                                                  
CONECT    5    4    6    8                                                  
CONECT    6    1    7    5                                                  
CONECT    7    6   10                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10   49                                                  
CONECT   10    9    7   11                                                  
CONECT   11   10   13   14                                                  
CONECT   12   13   16   17                                                  
CONECT   13   11   12                                                       
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12   18                                                  
CONECT   17   12                                                            
CONECT   18   16                                                            
CONECT   19    2                                                            
CONECT   20   21   25                                                       
CONECT   21   20   22   30                                                  
CONECT   22   21   23   29                                                  
CONECT   23   22   24   28                                                  
CONECT   24   23   25   27                                                  
CONECT   25   24   20   26                                                  
CONECT   26    4   25                                                       
CONECT   27   24                                                            
CONECT   28   23                                                            
CONECT   29   22                                                            
CONECT   30   21   31                                                       
CONECT   31   30                                                            
CONECT   32   33   37                                                       
CONECT   33   32   34   41                                                  
CONECT   34   33   35   40                                                  
CONECT   35   34   36   39                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36   32   50                                                  
CONECT   38   36                                                            
CONECT   39   35                                                            
CONECT   40   34                                                            
CONECT   41   33   42                                                       
CONECT   42   41                                                            
CONECT   43   44   48                                                       
CONECT   44   43   45   53                                                  
CONECT   45   44   46   52                                                  
CONECT   46   45   47   51                                                  
CONECT   47   46   48   50                                                  
CONECT   48   47   43   49                                                  
CONECT   49    9   48                                                       
CONECT   50   37   47                                                       
CONECT   51   46                                                            
CONECT   52   45                                                            
CONECT   53   44   59                                                       
CONECT   54   55                                                            
CONECT   55   54   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55   58                                                       
CONECT   58   57   59   60                                                  
CONECT   59   53   58                                                       
CONECT   60   58                                                            
MASTER        0    0    0    0    0    0    0    0   60    0  130    0
END

Download
3D PDB for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)
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SMILES for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)
OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](COC(=O)CC(O)=O)O[C@H]2OC2=CC3=C(C=C(O)C=C3O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@@H](O)[C@@H]1O
Download
INCHI for NP0048965 (Cyanidin 3-(malonylsophoroside) 5-glucoside)
InChI=1S/C36H42O24/c37-8-19-24(45)27(48)30(51)34(57-19)55-17-5-12(39)4-16-13(17)6-18(32(54-16)11-1-2-14(40)15(41)3-11)56-36-33(60-35-31(52)28(49)25(46)20(9-38)58-35)29(50)26(47)21(59-36)10-53-23(44)7-22(42)43/h1-6,19-21,24-31,33-38,45-52H,7-10H2,(H3-,39,40,41,42,43)/p+1/t19-,20-,21-,24-,25-,26-,27+,28+,29+,30-,31-,33-,34-,35+,36-/m1/s1
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View in JSmol
Synonyms
ValueSource
Cyanidin 3-(6''-malonylsophoroside)-5-glucosideHMDB
Chemical FormulaC36H43O24
Average Mass859.7122 Da
Monoisotopic Mass859.21443 Da
IUPAC Name3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-4,5-dihydroxy-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
Traditional Name3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-4,5-dihydroxy-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
CAS Registry Number63003-09-8
SMILES
OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](COC(=O)CC(O)=O)O[C@H]2OC2=CC3=C(C=C(O)C=C3O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C36H42O24/c37-8-19-24(45)27(48)30(51)34(57-19)55-17-5-12(39)4-16-13(17)6-18(32(54-16)11-1-2-14(40)15(41)3-11)56-36-33(60-35-31(52)28(49)25(46)20(9-38)58-35)29(50)26(47)21(59-36)10-53-23(44)7-22(42)43/h1-6,19-21,24-31,33-38,45-52H,7-10H2,(H3-,39,40,41,42,43)/p+1/t19-,20-,21-,24-,25-,26-,27+,28+,29+,30-,31-,33-,34-,35+,36-/m1/s1
InChI KeyASCBTZBIOSPIRQ-DTYOCLMRSA-O
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Brassica oleraceaPlant
Brassica oleracea var. botrytisFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as anthocyanidin-5-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C5-position.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavonoid glycosides  
Direct ParentAnthocyanidin-5-O-glycosides  
Alternative Parents
Substituents
  • Anthocyanidin-3-o-glycoside
    • 

  • Anthocyanidin-5-o-glycoside
    • 

  • Flavonoid-3-o-glycoside
    • 

  • 3'-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • Hydroxyflavonoid
    • 

  • Anthocyanidin
    • 

  • Phenolic glycoside
    • 

  • Disaccharide
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Benzopyran
    • 

  • 1-benzopyran
    • 

  • Catechol
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Phenol
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1,3-dicarbonyl compound
    • 

  • Oxane
    • 

  • Monocyclic benzene moiety
    • 

  • Benzenoid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Heteroaromatic compound
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Organic cation
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.22ALOGPS
logP-4.1ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)3.29ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area395.11 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity196.31 m³·mol⁻¹ChemAxon
Polarizability80.01 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0037981  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB017168  
KNApSAcK IDC00006841  
Chemspider ID30777222  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound126455742  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available