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Showing NP-Card for Peonidin 3-xyloside (NP0339429)

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Record Information
Version2.0
Created at2024-09-11 21:48:19 UTC
Updated at2024-09-11 21:48:19 UTC
NP-MRD IDNP0339429
Secondary Accession NumbersNone
Natural Product Identification
Common NamePeonidin 3-xyloside
DescriptionPeonidin 3-xyloside 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. Peonidin 3-xyloside is a polyphenol metabolite detected in biological fluids. Peonidin 3-xyloside is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339429 (Peonidin 3-xyloside)


  Mrv0541 02271201312D          

 31 34  0  0  1  0            999 V2000
    1.4289    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.9875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    2.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    3.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.6375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.6375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2869    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2869    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.4000    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.5599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.3445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3020   -1.3445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0471   -0.5599    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.0750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7375   -0.3049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1829   -2.0120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119   -2.0120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2763   -2.7656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 14 21  1  0  0  0  0
 21 22  2  0  0  0  0
 10 22  1  0  0  0  0
 27 12  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 23 27  1  0  0  0  0
 26 28  1  6  0  0  0
 25 29  1  1  0  0  0
 24 30  1  1  0  0  0
 30 31  1  0  0  0  0
M  CHG  1  22   1
M  END
Download

3D MOL for NP0339429 (Peonidin 3-xyloside)

Download
3D SDF for NP0339429 (Peonidin 3-xyloside)

  Mrv0541 02271201312D          

 31 34  0  0  1  0            999 V2000
    1.4289    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.9875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    2.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    3.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.6375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.6375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.2250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2869    1.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2869    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    1.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.4000    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.5599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.3445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3020   -1.3445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0471   -0.5599    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.0750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7375   -0.3049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1829   -2.0120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119   -2.0120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2763   -2.7656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 14 21  1  0  0  0  0
 21 22  2  0  0  0  0
 10 22  1  0  0  0  0
 27 12  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 23 27  1  0  0  0  0
 26 28  1  6  0  0  0
 25 29  1  1  0  0  0
 24 30  1  1  0  0  0
 30 31  1  0  0  0  0
M  CHG  1  22   1
M  END
> <DATABASE_ID>
NP0339429

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=CC(=C1)C1=C(O[C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)C=C2C(O)=CC(O)=CC2=[O+]1

> <INCHI_IDENTIFIER>
InChI=1S/C21H20O10/c1-28-15-4-9(2-3-12(15)24)20-16(30-21-19(27)18(26)17(8-22)31-21)7-11-13(25)5-10(23)6-14(11)29-20/h2-7,17-19,21-22,26-27H,8H2,1H3,(H2-,23,24,25)/p+1/t17-,18+,19-,21-/m1/s1

> <INCHI_KEY>
KGHFAKPGOXLHAB-RCLSDMTESA-O

> <FORMULA>
C21H21O10

> <MOLECULAR_WEIGHT>
433.3854

> <EXACT_MASS>
433.113471892

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
42.39425306954738

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-{[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium

> <ALOGPS_LOGP>
1.10

> <JCHEM_LOGP>
1.0912000000000002

> <ALOGPS_LOGS>
-3.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.538795589957727

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.3955253035299835

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811524252368704

> <JCHEM_POLAR_SURFACE_AREA>
162.21

> <JCHEM_REFRACTIVITY>
114.7773

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.94e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0339429 (Peonidin 3-xyloside)
Download
PDB for NP0339429 (Peonidin 3-xyloside)
HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1  C   UNK     0       2.667   2.170   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667   3.710   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   4.480   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   6.020   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667   6.790   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000   6.790   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334   6.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   4.480   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   3.710   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667   3.710   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   2.170   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334   1.400   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -4.001   1.400   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335   2.170   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.668   1.400   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -6.668  -0.140   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -8.002   2.170   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -8.002   3.710   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -9.336   4.480   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -6.668   4.480   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.335   3.710   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.001   4.480   0.000  0.00  0.00           O+1
HETATM   23  O   UNK     0      -2.580  -1.045   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -2.104  -2.510   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.564  -2.510   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.088  -1.045   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.334  -0.140   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.377  -0.569   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.341  -3.756   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -3.009  -3.756   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -2.382  -5.162   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11   22                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11   27                                                       
CONECT   13   11   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   14   22                                                  
CONECT   22   21   10                                                       
CONECT   23   24   27                                                       
CONECT   24   23   25   30                                                  
CONECT   25   24   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   12   26   23                                                  
CONECT   28   26                                                            
CONECT   29   25                                                            
CONECT   30   24   31                                                       
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   68    0
END

Download
3D PDB for NP0339429 (Peonidin 3-xyloside)
Download
SMILES for NP0339429 (Peonidin 3-xyloside)
COC1=C(O)C=CC(=C1)C1=C(O[C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)C=C2C(O)=CC(O)=CC2=[O+]1
Download
INCHI for NP0339429 (Peonidin 3-xyloside)
InChI=1S/C21H20O10/c1-28-15-4-9(2-3-12(15)24)20-16(30-21-19(27)18(26)17(8-22)31-21)7-11-13(25)5-10(23)6-14(11)29-20/h2-7,17-19,21-22,26-27H,8H2,1H3,(H2-,23,24,25)/p+1/t17-,18+,19-,21-/m1/s1
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View in JSmol
Synonyms
ValueSource
Peonidin 3-O-xylosideHMDB
Chemical FormulaC21H21O10
Average Mass433.3854 Da
Monoisotopic Mass433.11347 Da
IUPAC Name3-{[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium
Traditional Name3-{[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
COC1=C(O)C=CC(=C1)C1=C(O[C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)C=C2C(O)=CC(O)=CC2=[O+]1
InChI Identifier
InChI=1S/C21H20O10/c1-28-15-4-9(2-3-12(15)24)20-16(30-21-19(27)18(26)17(8-22)31-21)7-11-13(25)5-10(23)6-14(11)29-20/h2-7,17-19,21-22,26-27H,8H2,1H3,(H2-,23,24,25)/p+1/t17-,18+,19-,21-/m1/s1
InChI KeyKGHFAKPGOXLHAB-RCLSDMTESA-O
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavonoid glycosides  
Direct ParentAnthocyanidin-3-O-glycosides  
Alternative Parents
Substituents
  • Anthocyanidin-3-o-glycoside
    • 

  • Flavonoid-3-o-glycoside
    • 

  • 3p-methoxyflavonoid-skeleton
    • 

  • Hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • 5-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • Anthocyanidin
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Benzopyran
    • 

  • Methoxyphenol
    • 

  • Pentose monosaccharide
    • 

  • 1-benzopyran
    • 

  • Phenoxy compound
    • 

  • Phenol ether
    • 

  • Anisole
    • 

  • Methoxybenzene
    • 

  • Phenol
    • 

  • Alkyl aryl ether
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • Monosaccharide
    • 

  • Monocyclic benzene moiety
    • 

  • Benzenoid
    • 

  • Heteroaromatic compound
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Acetal
    • 

  • Organoheterocyclic compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • 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
logP1.1ALOGPS
logP1.09ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)6.4ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area162.21 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity114.78 m³·mol⁻¹ChemAxon
Polarizability42.39 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041767  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029938  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131753205  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References