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Showing NP-Card for Cyanidin 3-O-xyloside (NP0341335)

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Record Information
Version2.0
Created at2024-09-12 08:41:14 UTC
Updated at2024-09-12 08:41:14 UTC
NP-MRD IDNP0341335
Secondary Accession NumbersNone
Natural Product Identification
Common NameCyanidin 3-O-xyloside
Description 3-{[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-ylium is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0341335 (Cyanidin 3-O-xyloside)

Cyanidin 3-0-xyloside
  Mrv1652304022019382D          

 30 33  0  0  1  0            999 V2000
   -1.0164   -3.7445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5315   -4.4120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8671   -5.1657    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7615   -2.9599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4749    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964   -2.9599    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8809   -2.7050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -3.7445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3264   -4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  2  0  0  0  0
  7 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 26  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
  1 29  1  0  0  0  0
 29 30  1  1  0  0  0
M  CHG  1  17   1
M  END
Download

3D MOL for NP0341335 (Cyanidin 3-O-xyloside)

Download
3D SDF for NP0341335 (Cyanidin 3-O-xyloside)
Cyanidin 3-0-xyloside
  Mrv1652304022019382D          

 30 33  0  0  1  0            999 V2000
   -1.0164   -3.7445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5315   -4.4120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8671   -5.1657    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7615   -2.9599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4749    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964   -2.9599    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8809   -2.7050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -3.7445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3264   -4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  2  0  0  0  0
  7 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 26  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
  1 29  1  0  0  0  0
 29 30  1  1  0  0  0
M  CHG  1  17   1
M  END
> <DATABASE_ID>
NP0341335

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H18O10/c21-7-16-17(26)18(27)20(30-16)29-15-6-10-12(24)4-9(22)5-14(10)28-19(15)8-1-2-11(23)13(25)3-8/h1-6,16-18,20-21,26-27H,7H2,(H3-,22,23,24,25)/p+1/t16-,17-,18-,20-/m1/s1

> <INCHI_KEY>
SBBFXSBQYRSIPP-SOAMZJECSA-O

> <FORMULA>
C20H19O10

> <MOLECULAR_WEIGHT>
419.361

> <EXACT_MASS>
419.097273232

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
40.40742074013784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-{[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
1.45

> <JCHEM_LOGP>
1.0594999999999994

> <ALOGPS_LOGS>
-3.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.457962066012987

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.388329710176589

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811524252368704

> <JCHEM_POLAR_SURFACE_AREA>
173.20999999999998

> <JCHEM_REFRACTIVITY>
110.295

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.06e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0341335 (Cyanidin 3-O-xyloside)
Download
PDB for NP0341335 (Cyanidin 3-O-xyloside)
HEADER    PROTEIN                                 02-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Cyanidin 3-0-xyloside                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-APR-20         0                                  
HETATM    1  C   UNK     0      -1.897  -6.990   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.992  -8.236   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.619  -9.643   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -1.421  -5.525   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+1
HETATM   18  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -6.668   2.310   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.913  -5.525   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -5.378  -5.049   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -3.437  -6.990   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -4.343  -8.236   0.000  0.00  0.00           O+0
CONECT    1    2    4   29                                                  
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6   27                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    9   16                                                  
CONECT   16   15                                                            
CONECT   17   10   18                                                       
CONECT   18   17    7   19                                                  
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   19                                                       
CONECT   27    5   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27    1   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

Download
3D PDB for NP0341335 (Cyanidin 3-O-xyloside)
Download
SMILES for NP0341335 (Cyanidin 3-O-xyloside)
OC[C@H]1O[C@@H](OC2=CC3=C(C=C(O)C=C3O)[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@@H]1O
Download
INCHI for NP0341335 (Cyanidin 3-O-xyloside)
InChI=1S/C20H18O10/c21-7-16-17(26)18(27)20(30-16)29-15-6-10-12(24)4-9(22)5-14(10)28-19(15)8-1-2-11(23)13(25)3-8/h1-6,16-18,20-21,26-27H,7H2,(H3-,22,23,24,25)/p+1/t16-,17-,18-,20-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC20H19O10
Average Mass419.3610 Da
Monoisotopic Mass419.09727 Da
IUPAC Name3-{[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium
Traditional Name3-{[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
OC[C@H]1O[C@@H](OC2=CC3=C(C=C(O)C=C3O)[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C20H18O10/c21-7-16-17(26)18(27)20(30-16)29-15-6-10-12(24)4-9(22)5-14(10)28-19(15)8-1-2-11(23)13(25)3-8/h1-6,16-18,20-21,26-27H,7H2,(H3-,22,23,24,25)/p+1/t16-,17-,18-,20-/m1/s1
InChI KeySBBFXSBQYRSIPP-SOAMZJECSA-O
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
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
logP1.45ALOGPS
logP1.06ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)6.39ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area173.21 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity110.3 m³·mol⁻¹ChemAxon
Polarizability40.41 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available