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Showing NP-Card for Cyanidin 3-O-arabinoside (NP0340019)

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Record Information
Version2.0
Created at2024-09-12 01:02:13 UTC
Updated at2024-09-12 01:02:14 UTC
NP-MRD IDNP0340019
Secondary Accession NumbersNone
Natural Product Identification
Common NameCyanidin 3-O-arabinoside
Description2-(3,4-Dihydroxyphenyl)-5,7-dihydroxy-3-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}-1λ⁴-chromen-1-ylium belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position. 2-(3,4-Dihydroxyphenyl)-5,7-dihydroxy-3-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}-1λ⁴-chromen-1-ylium is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0340019 (Cyanidin 3-O-arabinoside)

Cyanidin 3-arabinoside
  Mrv1652304022019382D          

 30 33  0  0  1  0            999 V2000
   11.2562   -6.2562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2562   -7.0812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.5417   -5.8437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5417   -7.4937    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8272   -6.2562    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8272   -7.0812    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9707   -7.4937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5417   -8.3187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1128   -7.4937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9845   -4.5208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9845   -5.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2699   -4.1083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2699   -5.7583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5555   -4.5208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5555   -5.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6989   -4.1084    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    8.4134   -4.5209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6989   -5.7583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4133   -5.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1278   -4.1084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1279   -3.2834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8424   -4.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8425   -2.8710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5568   -4.1086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5569   -3.2836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2714   -2.8711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2699   -6.5833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8410   -4.1083    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1285   -5.7444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2713   -4.5211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
 12 10  2  0  0  0  0
 13 11  2  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 15 14  2  0  0  0  0
 16 10  1  0  0  0  0
 11 10  1  0  0  0  0
 17 16  2  0  0  0  0
 18 11  1  0  0  0  0
 19 17  1  0  0  0  0
 19 18  2  0  0  0  0
 21 20  1  0  0  0  0
 22 20  2  0  0  0  0
 23 21  2  0  0  0  0
 24 22  1  0  0  0  0
 25 23  1  0  0  0  0
 25 24  2  0  0  0  0
 17 20  1  0  0  0  0
 25 26  1  0  0  0  0
 13 27  1  0  0  0  0
 14 28  1  0  0  0  0
 19 29  1  0  0  0  0
 24 30  1  0  0  0  0
  4  8  1  6  0  0  0
  6  9  1  1  0  0  0
  5 29  1  1  0  0  0
  2  7  1  6  0  0  0
M  CHG  1  16   1
M  END
Download

3D MOL for NP0340019 (Cyanidin 3-O-arabinoside)

Download
3D SDF for NP0340019 (Cyanidin 3-O-arabinoside)
Cyanidin 3-arabinoside
  Mrv1652304022019382D          

 30 33  0  0  1  0            999 V2000
   11.2562   -6.2562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2562   -7.0812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.5417   -5.8437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5417   -7.4937    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8272   -6.2562    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8272   -7.0812    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9707   -7.4937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5417   -8.3187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1128   -7.4937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9845   -4.5208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9845   -5.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2699   -4.1083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2699   -5.7583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5555   -4.5208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5555   -5.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6989   -4.1084    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    8.4134   -4.5209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6989   -5.7583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4133   -5.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1278   -4.1084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1279   -3.2834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8424   -4.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8425   -2.8710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5568   -4.1086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5569   -3.2836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2714   -2.8711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2699   -6.5833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8410   -4.1083    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1285   -5.7444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2713   -4.5211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
 12 10  2  0  0  0  0
 13 11  2  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 15 14  2  0  0  0  0
 16 10  1  0  0  0  0
 11 10  1  0  0  0  0
 17 16  2  0  0  0  0
 18 11  1  0  0  0  0
 19 17  1  0  0  0  0
 19 18  2  0  0  0  0
 21 20  1  0  0  0  0
 22 20  2  0  0  0  0
 23 21  2  0  0  0  0
 24 22  1  0  0  0  0
 25 23  1  0  0  0  0
 25 24  2  0  0  0  0
 17 20  1  0  0  0  0
 25 26  1  0  0  0  0
 13 27  1  0  0  0  0
 14 28  1  0  0  0  0
 19 29  1  0  0  0  0
 24 30  1  0  0  0  0
  4  8  1  6  0  0  0
  6  9  1  1  0  0  0
  5 29  1  1  0  0  0
  2  7  1  6  0  0  0
M  CHG  1  16   1
M  END
> <DATABASE_ID>
NP0340019

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CO[C@H](OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H18O10/c21-9-4-12(23)10-6-16(30-20-18(27)17(26)14(25)7-28-20)19(29-15(10)5-9)8-1-2-11(22)13(24)3-8/h1-6,14,17-18,20,25-27H,7H2,(H3-,21,22,23,24)/p+1/t14-,17-,18+,20+/m0/s1

> <INCHI_KEY>
KUCVMQMKRICXJC-FEUVXWNVSA-O

> <FORMULA>
C20H19O10

> <MOLECULAR_WEIGHT>
419.361

> <EXACT_MASS>
419.097273232

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
39.995557006783805

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
1.37

> <JCHEM_LOGP>
1.0594999999999994

> <ALOGPS_LOGS>
-3.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.4579651225779635

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.388332879836749

> <JCHEM_PKA_STRONGEST_BASIC>
-3.52659856908344

> <JCHEM_POLAR_SURFACE_AREA>
173.20999999999998

> <JCHEM_REFRACTIVITY>
110.295

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.56e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0340019 (Cyanidin 3-O-arabinoside)
Download
PDB for NP0340019 (Cyanidin 3-O-arabinoside)
HEADER    PROTEIN                                 02-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Cyanidin 3-arabinoside                            
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-APR-20         0                                  
HETATM    1  C   UNK     0      21.012 -11.678   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.012 -13.218   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      19.678 -10.908   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      19.678 -13.988   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.344 -11.678   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.344 -13.218   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      22.345 -13.988   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      19.678 -15.528   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      17.011 -13.988   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      13.038  -8.439   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.038  -9.979   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.704  -7.669   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.704 -10.749   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.370  -8.439   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.370  -9.979   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      14.371  -7.669   0.000  0.00  0.00           O+1
HETATM   17  C   UNK     0      15.705  -8.439   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.371 -10.749   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      15.705  -9.979   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      17.039  -7.669   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      17.039  -6.129   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      18.372  -8.439   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      18.373  -5.359   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      19.706  -7.669   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      19.706  -6.129   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      21.040  -5.359   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      11.704 -12.289   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       9.037  -7.669   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      17.040 -10.723   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      21.040  -8.439   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    7                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6    8                                                  
CONECT    5    3    6   29                                                  
CONECT    6    4    5    9                                                  
CONECT    7    2                                                            
CONECT    8    4                                                            
CONECT    9    6                                                            
CONECT   10   12   16   11                                                  
CONECT   11   13   10   18                                                  
CONECT   12   10   14                                                       
CONECT   13   11   15   27                                                  
CONECT   14   12   15   28                                                  
CONECT   15   13   14                                                       
CONECT   16   10   17                                                       
CONECT   17   16   19   20                                                  
CONECT   18   11   19                                                       
CONECT   19   17   18   29                                                  
CONECT   20   21   22   17                                                  
CONECT   21   20   23                                                       
CONECT   22   20   24                                                       
CONECT   23   21   25                                                       
CONECT   24   22   25   30                                                  
CONECT   25   23   24   26                                                  
CONECT   26   25                                                            
CONECT   27   13                                                            
CONECT   28   14                                                            
CONECT   29   19    5                                                       
CONECT   30   24                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

Download
3D PDB for NP0340019 (Cyanidin 3-O-arabinoside)
Download
SMILES for NP0340019 (Cyanidin 3-O-arabinoside)
O[C@H]1CO[C@H](OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@H]1O
Download
INCHI for NP0340019 (Cyanidin 3-O-arabinoside)
InChI=1S/C20H18O10/c21-9-4-12(23)10-6-16(30-20-18(27)17(26)14(25)7-28-20)19(29-15(10)5-9)8-1-2-11(22)13(24)3-8/h1-6,14,17-18,20,25-27H,7H2,(H3-,21,22,23,24)/p+1/t14-,17-,18+,20+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC20H19O10
Average Mass419.3610 Da
Monoisotopic Mass419.09727 Da
IUPAC Name2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}-1lambda4-chromen-1-ylium
Traditional Name2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-{[(2R,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}-1lambda4-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
O[C@H]1CO[C@H](OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C20H18O10/c21-9-4-12(23)10-6-16(30-20-18(27)17(26)14(25)7-28-20)19(29-15(10)5-9)8-1-2-11(22)13(24)3-8/h1-6,14,17-18,20,25-27H,7H2,(H3-,21,22,23,24)/p+1/t14-,17-,18+,20+/m0/s1
InChI KeyKUCVMQMKRICXJC-FEUVXWNVSA-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 flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavonoid glycosides  
Direct ParentFlavonoid-3-O-glycosides  
Alternative Parents
Substituents
  • Flavonoid-3-o-glycoside
    • 

  • 5-hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • 3'-hydroxyflavonoid
    • 

  • Hydroxyflavonoid
    • 

  • Anthocyanidin
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Benzopyran
    • 

  • 1-benzopyran
    • 

  • Catechol
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Phenol
    • 

  • Monocyclic benzene moiety
    • 

  • Benzenoid
    • 

  • Monosaccharide
    • 

  • Oxane
    • 

  • Heteroaromatic compound
    • 

  • Secondary alcohol
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Organooxygen 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
logP1.37ALOGPS
logP1.06ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)6.39ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area173.21 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity110.3 m³·mol⁻¹ChemAxon
Polarizability40 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