NP-MRD: Showing NP-Card for 5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one (NP0149398)

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Record Information

Version

2.0

Created at

2022-09-02 05:17:05 UTC

Updated at

2022-09-02 05:17:05 UTC

NP-MRD ID

NP0149398

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one

Description

Ikarisoside a 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. Thus, ikarisoside a is considered to be a flavonoid. 5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one is found in Epimedium diphyllum, Epimedium sagittatum, Epimedium sempervirens and Epimedium wushanense. 5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one was first documented in 2008 (PMID: 18929556). Based on a literature review a small amount of articles have been published on Ikarisoside a (PMID: 26257152) (PMID: 29575004) (PMID: 23228597) (PMID: 20353769).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022207172D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309022207172D          

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M  END
> <DATABASE_ID>
NP0149398

> <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]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O10/c1-11(2)4-9-15-16(28)10-17(29)18-20(31)25(36-26-22(33)21(32)19(30)12(3)34-26)23(35-24(15)18)13-5-7-14(27)8-6-13/h4-8,10,12,19,21-22,26-30,32-33H,9H2,1-3H3/t12-,19-,21+,22+,26-/m0/s1

> <INCHI_KEY>
RPLMLWBOUPDPQF-GULSFEPBSA-N

> <FORMULA>
C26H28O10

> <MOLECULAR_WEIGHT>
500.5

> <EXACT_MASS>
500.168247102

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
50.92977497905787

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.50

> <JCHEM_LOGP>
2.9342069916666667

> <ALOGPS_LOGS>
-3.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.831180502240299

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.206626491612767

> <JCHEM_PKA_STRONGEST_BASIC>
-3.612200408172593

> <JCHEM_POLAR_SURFACE_AREA>
166.14

> <JCHEM_REFRACTIVITY>
129.99370000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.83e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   36                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   36                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   27                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   17   26                                                  
CONECT   26   25                                                            
CONECT   27   15   28   35                                                  
CONECT   28   27   29   34                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   28                                                       
CONECT   35   27   36                                                       
CONECT   36   35    6   12                                                  
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₀

Average Mass

500.5000 Da

Monoisotopic Mass

500.16825 Da

IUPAC Name

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

Traditional Name

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

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]1O

InChI Identifier

InChI=1S/C26H28O10/c1-11(2)4-9-15-16(28)10-17(29)18-20(31)25(36-26-22(33)21(32)19(30)12(3)34-26)23(35-24(15)18)13-5-7-14(27)8-6-13/h4-8,10,12,19,21-22,26-30,32-33H,9H2,1-3H3/t12-,19-,21+,22+,26-/m0/s1

InChI Key

RPLMLWBOUPDPQF-GULSFEPBSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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 sagittatum	LOTUS Database	35616633
Epimedium sempervirens	LOTUS Database	35616633
Epimedium wushanense	LOTUS Database	35616633

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
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavone
Hydroxyflavonoid
Hexose monosaccharide
Chromone
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Pyran
Oxane
Monocyclic benzene moiety
Monosaccharide
Benzenoid
Vinylogous acid
Heteroaromatic compound
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
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	2.5	ALOGPS
logP	2.93	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	6.21	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	166.14 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	129.99 m³·mol⁻¹	ChemAxon
Polarizability	50.93 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00005805

Chemspider ID

4587709

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5481982

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li X, Toyohira Y, Horisita T, Satoh N, Takahashi K, Zhang H, Iinuma M, Yoshinaga Y, Ueno S, Tsutsui M, Sata T, Yanagihara N: Ikarisoside A inhibits acetylcholine-induced catecholamine secretion and synthesis by suppressing nicotinic acetylcholine receptor-ion channels in cultured bovine adrenal medullary cells. Naunyn Schmiedebergs Arch Pharmacol. 2015 Dec;388(12):1259-69. doi: 10.1007/s00210-015-1161-y. Epub 2015 Aug 11. [PubMed:26257152 ]
Cong Y, Wang R, Zhang C, Lin H: A simple and selective LC-MS/MS method for quantification of ikarisoside A in rat plasma and its application to a pharmacokinetic study. Biomed Chromatogr. 2018 Aug;32(8):e4245. doi: 10.1002/bmc.4245. Epub 2018 Apr 23. [PubMed:29575004 ]
Endo S, Matsunaga T, Fujimoto A, Kumada S, Arai Y, Miura Y, Mikamo H, El-Kabbani O, Yamano S, Iinuma M, Hara A: Characterization of rabbit morphine 6-dehydrogenase and two NAD(+)-dependent 3alpha(17beta)-hydroxysteroid dehydrogenases. Arch Biochem Biophys. 2013 Jan 15;529(2):131-9. doi: 10.1016/j.abb.2012.11.013. Epub 2012 Dec 7. [PubMed:23228597 ]
Choi HJ, Park YR, Nepal M, Choi BY, Cho NP, Choi SH, Heo SR, Kim HS, Yang MS, Soh Y: Inhibition of osteoclastogenic differentiation by Ikarisoside A in RAW 264.7 cells via JNK and NF-kappaB signaling pathways. Eur J Pharmacol. 2010 Jun 25;636(1-3):28-35. doi: 10.1016/j.ejphar.2010.03.023. Epub 2010 Mar 29. [PubMed:20353769 ]
Choi HJ, Eun JS, Park YR, Kim DK, Li R, Moon WS, Park JM, Kim HS, Cho NP, Cho SD, Soh Y: Ikarisoside A inhibits inducible nitric oxide synthase in lipopolysaccharide-stimulated RAW 264.7 cells via p38 kinase and nuclear factor-kappaB signaling pathways. Eur J Pharmacol. 2008 Dec 28;601(1-3):171-8. doi: 10.1016/j.ejphar.2008.09.032. Epub 2008 Sep 30. [PubMed:18929556 ]
LOTUS database [Link]

Showing NP-Card for 5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one (NP0149398)

MOL for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

3D MOL for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

3D SDF for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

3D-SDF for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

PDB for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

3D PDB for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

SMILES for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

INCHI for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

Structure for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)

3D Structure for NP0149398 (5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-3-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one)