NP-MRD: Showing NP-Card for Ikarisoside D (NP0054004)

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Record Information

Version

2.0

Created at

2022-04-28 00:29:43 UTC

Updated at

2022-04-28 00:29:43 UTC

NP-MRD ID

NP0054004

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ikarisoside D

Description

(2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxo-4H-chromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetate 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. Ikarisoside D is found in Epimedium diphyllum and Epimedium grandiflorum . Based on a literature review very few articles have been published on (2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxo-4H-chromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282202292D          

 39 42  0  0  1  0            999 V2000
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    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   -1.2375    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
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -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
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  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  5 12  1  0  0  0  0
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  4 15  1  0  0  0  0
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 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
  3 38  1  0  0  0  0
  1 39  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282202292D          

 39 42  0  0  1  0            999 V2000
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 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
  4 15  1  0  0  0  0
 15 16  2  0  0  0  0
 14 17  1  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 18 23  1  0  0  0  0
 23 24  1  1  0  0  0
 22 25  1  1  0  0  0
 21 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 20 30  1  6  0  0  0
 13 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
  3 38  1  0  0  0  0
  1 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054004

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@@H](OC2=C(OC3=C(CC=C(C)C)C(O)=CC(O)=C3C2=O)C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@H]1OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H30O11/c1-12(2)5-10-17-18(31)11-19(32)20-21(33)27(25(38-26(17)20)15-6-8-16(30)9-7-15)39-28-23(35)22(34)24(13(3)36-28)37-14(4)29/h5-9,11,13,22-24,28,30-32,34-35H,10H2,1-4H3/t13-,22+,23-,24-,28-/m0/s1

> <INCHI_KEY>
ZVEFBUCBFFPLIG-SYJMSKJASA-N

> <FORMULA>
C28H30O11

> <MOLECULAR_WEIGHT>
542.537

> <EXACT_MASS>
542.178811786

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
54.36835216297365

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxo-4H-chromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetate

> <ALOGPS_LOGP>
3.21

> <JCHEM_LOGP>
3.3753324019999997

> <ALOGPS_LOGS>
-3.55

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.831182297971851

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.2066265346005265

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6916111614138982

> <JCHEM_POLAR_SURFACE_AREA>
172.20999999999998

> <JCHEM_REFRACTIVITY>
139.1452

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.52e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxochromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetate

> <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  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+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       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   39                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   38                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    5   13                                                       
CONECT   13   12   14   31                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14    4   16                                                  
CONECT   16   15                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   30                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23   25                                                  
CONECT   23   22   18   24                                                  
CONECT   24   23                                                            
CONECT   25   22                                                            
CONECT   26   21   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   20                                                            
CONECT   31   13   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   34                                                            
CONECT   38    3                                                            
CONECT   39    1                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxo-4H-chromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetic acid	Generator

Chemical Formula

C₂₈H₃₀O₁₁

Average Mass

542.5370 Da

Monoisotopic Mass

542.17881 Da

IUPAC Name

(2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxo-4H-chromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetate

Traditional Name

(2S,3R,4R,5S,6S)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-4-oxochromen-3-yl]oxy}-4,5-dihydroxy-2-methyloxan-3-yl acetate

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](OC2=C(OC3=C(CC=C(C)C)C(O)=CC(O)=C3C2=O)C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@H]1OC(C)=O

InChI Identifier

InChI=1S/C28H30O11/c1-12(2)5-10-17-18(31)11-19(32)20-21(33)27(25(38-26(17)20)15-6-8-16(30)9-7-15)39-28-23(35)22(34)24(13(3)36-28)37-14(4)29/h5-9,11,13,22-24,28,30-32,34-35H,10H2,1-4H3/t13-,22+,23-,24-,28-/m0/s1

InChI Key

ZVEFBUCBFFPLIG-SYJMSKJASA-N

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
Epimedium diphyllum	LOTUS Database	35616633
Epimedium grandiflorum	Plant	KNApSAcK

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.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-3-O-glycosides

Alternative Parents

Substituents

Flavonoid-3-o-glycoside
8-prenylated flavone
Hydroxyflavonoid
Flavone
7-hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Chromone
1-benzopyran
Benzopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Phenol
Benzenoid
Pyran
Oxane
Monosaccharide
Monocyclic benzene moiety
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Carboxylic acid ester
1,2-diol
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	3.21	ALOGPS
logP	3.38	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	6.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	172.21 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	139.15 m³·mol⁻¹	ChemAxon
Polarizability	54.37 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162977642

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Ikarisoside D (NP0054004)

MOL for NP0054004 (Ikarisoside D)

3D MOL for NP0054004 (Ikarisoside D)

3D SDF for NP0054004 (Ikarisoside D)

3D-SDF for NP0054004 (Ikarisoside D)

PDB for NP0054004 (Ikarisoside D)

3D PDB for NP0054004 (Ikarisoside D)

SMILES for NP0054004 (Ikarisoside D)

INCHI for NP0054004 (Ikarisoside D)

Structure for NP0054004 (Ikarisoside D)

3D Structure for NP0054004 (Ikarisoside D)