NP-MRD: Showing NP-Card for 5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one (NP0249529)

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Record Information

Version

2.0

Created at

2022-09-07 12:06:27 UTC

Updated at

2022-09-07 12:06:27 UTC

NP-MRD ID

NP0249529

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one

Description

5,7-Dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-4H-chromen-4-one 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. 5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one is found in Epimedium wushanense. 5,7-Dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-4H-chromen-4-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251511552D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251511552D          

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M  END
> <DATABASE_ID>
NP0249529

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(OC2=C(OC3=C(CC=C(C)C)C(O)=CC(O)=C3C2=O)C2=CC=CC=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O9/c1-12(2)9-10-15-16(27)11-17(28)18-20(30)25(23(34-24(15)18)14-7-5-4-6-8-14)35-26-22(32)21(31)19(29)13(3)33-26/h4-9,11,13,19,21-22,26-29,31-32H,10H2,1-3H3

> <INCHI_KEY>
VVWQFHBZEMQMDV-UHFFFAOYSA-N

> <FORMULA>
C26H28O9

> <MOLECULAR_WEIGHT>
484.501

> <EXACT_MASS>
484.173332482

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
49.30130062375742

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.41

> <JCHEM_LOGP>
3.237772313333333

> <ALOGPS_LOGS>
-3.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.922989738676118

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.208640709392629

> <JCHEM_PKA_STRONGEST_BASIC>
-3.612200408172593

> <JCHEM_POLAR_SURFACE_AREA>
145.91

> <JCHEM_REFRACTIVITY>
128.01280000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.43e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   30                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   22                                                  
CONECT    7    6    8   24                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   21                                                  
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   10   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19    9   22                                                  
CONECT   22   21    6   23                                                  
CONECT   23   22                                                            
CONECT   24    7   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30    4   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    2   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₉

Average Mass

484.5010 Da

Monoisotopic Mass

484.17333 Da

IUPAC Name

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

Traditional Name

5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one

CAS Registry Number

Not Available

SMILES

CC1OC(OC2=C(OC3=C(CC=C(C)C)C(O)=CC(O)=C3C2=O)C2=CC=CC=C2)C(O)C(O)C1O

InChI Identifier

InChI=1S/C26H28O9/c1-12(2)9-10-15-16(27)11-17(28)18-20(30)25(23(34-24(15)18)14-7-5-4-6-8-14)35-26-22(32)21(31)19(29)13(3)33-26/h4-9,11,13,19,21-22,26-29,31-32H,10H2,1-3H3

InChI Key

VVWQFHBZEMQMDV-UHFFFAOYSA-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 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

8-prenylated flavone
Flavonoid-3-o-glycoside
Hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavone
Hexose monosaccharide
O-glycosyl compound
Chromone
Glycosyl compound
Benzopyran
1-benzopyran
Pyranone
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Pyran
Monosaccharide
Benzenoid
Oxane
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Organooxygen compound
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	2.41	ALOGPS
logP	3.24	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	6.21	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	145.91 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	128.01 m³·mol⁻¹	ChemAxon
Polarizability	49.3 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one (NP0249529)

MOL for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

3D MOL for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

3D SDF for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

3D-SDF for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

PDB for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

3D PDB for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

SMILES for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

INCHI for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

Structure for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)

3D Structure for NP0249529 (5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2-phenyl-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]chromen-4-one)