NP-MRD: Showing NP-Card for Pelargonidin 3-glucoside-5-(6'''-malonylglucoside) (NP0054522)

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Record Information

Version

2.0

Created at

2022-04-28 00:51:04 UTC

Updated at

2022-04-28 00:51:04 UTC

NP-MRD ID

NP0054522

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pelargonidin 3-glucoside-5-(6'''-malonylglucoside)

Description

Pelargonidin 3-glucoside-5-(6'''-malonylglucoside) is found in Hyacinthus orientalis.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282202512D          

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  1 48  1  0  0  0  0
M  CHG  1   7   1
M  END

     RDKit          3D

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M  CHG  1  19   1
M  END


  Mrv1652304282202512D          

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    2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   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
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  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
  4 10  1  0  0  0  0
  9 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 17  1  0  0  0  0
 16 18  1  6  0  0  0
 18 19  1  0  0  0  0
 15 20  1  1  0  0  0
 14 21  1  6  0  0  0
 13 22  1  6  0  0  0
  8 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 23 28  1  0  0  0  0
 26 29  1  0  0  0  0
  3 30  1  0  0  0  0
 31 30  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 31 36  1  0  0  0  0
 35 37  1  1  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 39 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  2  0  0  0  0
 42 44  1  0  0  0  0
 34 45  1  6  0  0  0
 33 46  1  1  0  0  0
 32 47  1  6  0  0  0
  1 48  1  0  0  0  0
M  CHG  1   7   1
M  END
> <DATABASE_ID>
NP0054522

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=CC3=C(O[C@@H]4O[C@H](COC(=O)CC(O)=O)[C@@H](O)[C@H](O)[C@H]4O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C30H32O18/c31-9-18-22(37)24(39)26(41)30(47-18)46-17-7-14-15(44-28(17)11-1-3-12(32)4-2-11)5-13(33)6-16(14)45-29-27(42)25(40)23(38)19(48-29)10-43-21(36)8-20(34)35/h1-7,18-19,22-27,29-31,37-42H,8-10H2,(H2-,32,33,34,35)/p+1/t18-,19-,22-,23-,24+,25+,26+,27-,29-,30-/m1/s1

> <INCHI_KEY>
XAUWJGQEHRUDEM-QPHPHRJCSA-O

> <FORMULA>
C30H33O18

> <MOLECULAR_WEIGHT>
681.575

> <EXACT_MASS>
681.166140643

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
64.47794007766005

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxyphenyl)-3-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
0.56

> <JCHEM_LOGP>
-1.7034000000000002

> <ALOGPS_LOGS>
-2.89

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.660200542207495

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3242252030419723

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6491030300991723

> <JCHEM_POLAR_SURFACE_AREA>
295.72999999999996

> <JCHEM_REFRACTIVITY>
161.9166000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.25e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxyphenyl)-3-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -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  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+1
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0     -12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0     -10.669  -3.080   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      -5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   48                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   30                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   23                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   15   21                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   12                                                       
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20   15                                                            
CONECT   21   14                                                            
CONECT   22   13                                                            
CONECT   23    8   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   26                                                            
CONECT   30    3   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33   47                                                  
CONECT   33   32   34   46                                                  
CONECT   34   33   35   45                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35   31                                                       
CONECT   37   35   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   42                                                       
CONECT   42   41   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45   34                                                            
CONECT   46   33                                                            
CONECT   47   32                                                            
CONECT   48    1                                                            
MASTER        0    0    0    0    0    0    0    0   48    0  104    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₃O₁₈

Average Mass

681.5750 Da

Monoisotopic Mass

681.16614 Da

IUPAC Name

5-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxyphenyl)-3-{[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1lambda4-chromen-1-ylium

Traditional Name

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=CC3=C(O[C@@H]4O[C@H](COC(=O)CC(O)=O)[C@@H](O)[C@H](O)[C@H]4O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C30H32O18/c31-9-18-22(37)24(39)26(41)30(47-18)46-17-7-14-15(44-28(17)11-1-3-12(32)4-2-11)5-13(33)6-16(14)45-29-27(42)25(40)23(38)19(48-29)10-43-21(36)8-20(34)35/h1-7,18-19,22-27,29-31,37-42H,8-10H2,(H2-,32,33,34,35)/p+1/t18-,19-,22-,23-,24+,25+,26+,27-,29-,30-/m1/s1

InChI Key

XAUWJGQEHRUDEM-QPHPHRJCSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Hyacinthus orientalis	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	0.56	ALOGPS
logP	-1.7	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	3.32	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	295.73 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	161.92 m³·mol⁻¹	ChemAxon
Polarizability	64.48 Å³	ChemAxon
Number of Rings	5	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

Not Available

References

General References

Not Available

Showing NP-Card for Pelargonidin 3-glucoside-5-(6'''-malonylglucoside) (NP0054522)

MOL for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

3D MOL for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

3D SDF for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

3D-SDF for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

PDB for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

3D PDB for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

SMILES for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

INCHI for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

Structure for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))

3D Structure for NP0054522 (Pelargonidin 3-glucoside-5-(6'''-malonylglucoside))