NP-MRD: Showing NP-Card for Isosilybin (NP0136995)

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Record Information

Version

2.0

Created at

2022-05-30 16:38:27 UTC

Updated at

2022-05-30 16:38:27 UTC

NP-MRD ID

NP0136995

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Isosilybin

Description

Isosilybin belongs to the class of organic compounds known as flavonolignans. These are non-conventional lignans that derived from flavonoids. They are characterized by a p-dioxin ring substituted at one carbon atom by a C3C6 (phenylpropan) group and fused to the B-ring of the 2-phenylchromene moiety. Isosilybin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Isosilybin has been detected, but not quantified in, coffee and coffee products and green vegetables. Isosilybin is found in Anastatica hierochuntica and Silybum marianum. Isosilybin was first documented in 2007 (PMID: 17389612). This could make isosilybin a potential biomarker for the consumption of these foods (PMID: 18332867) (PMID: 20721970).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241218052D          

 35 39  0  0  0  0            999 V2000
   -2.5005    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5005    1.6501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2156    1.2376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9292    1.6501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9292    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6441   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9291   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2154   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5003   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5003   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2154   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9291   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.3592   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv0541 02241218052D          

 35 39  0  0  0  0            999 V2000
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   -2.5005    1.6501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2156    1.2376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9292    1.6501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0136995

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC=C1O)C1OC2=C(OC1CO)C=C(C=C2)C1OC2=C(C(O)=CC(O)=C2)C(=O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H22O10/c1-32-17-6-11(2-4-14(17)28)24-20(10-26)33-18-7-12(3-5-16(18)34-24)25-23(31)22(30)21-15(29)8-13(27)9-19(21)35-25/h2-9,20,23-29,31H,10H2,1H3

> <INCHI_KEY>
FDQAOULAVFHKBX-UHFFFAOYSA-N

> <FORMULA>
C25H22O10

> <MOLECULAR_WEIGHT>
482.4362

> <EXACT_MASS>
482.121296924

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
48.507654400100435

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,5,7-trihydroxy-2-[2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.35

> <JCHEM_LOGP>
2.6293160946666667

> <ALOGPS_LOGS>
-3.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.816800082471506

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.811772785042609

> <JCHEM_PKA_STRONGEST_BASIC>
-2.990414182412958

> <JCHEM_POLAR_SURFACE_AREA>
155.14000000000001

> <JCHEM_REFRACTIVITY>
120.29390000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.17e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,5,7-trihydroxy-2-[2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-2,3-dihydro-1-benzopyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -4.668   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.668   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.002   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -7.335   3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -7.335   4.620   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       8.669  -4.620   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       7.334  -3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.002  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.667  -3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.667  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.002  -1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.334  -2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       8.669  -1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.004  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -8.669   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.669   0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -7.335   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.002   0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -4.668   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0     -10.004   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.001   3.080   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -3.333   2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.333   0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.001   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.001  -1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.666  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.666  -1.540   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.001  -2.310   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.335  -1.540   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.667   2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.667   0.770   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.335   0.000   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.001   0.770   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.666   0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.666   0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4   18                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4                                                            
CONECT    6    7                                                            
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   29                                                  
CONECT   11   10   12                                                       
CONECT   12    7   11   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15    4   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18    3   17   19                                                  
CONECT   19   18   23                                                       
CONECT   20   16                                                            
CONECT   21   22                                                            
CONECT   22    2   21   23                                                  
CONECT   23   19   22   24                                                  
CONECT   24   23   25   35                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   10   28   32                                                  
CONECT   30   31                                                            
CONECT   31   30   32                                                       
CONECT   32   29   31   33                                                  
CONECT   33   32   34                                                       
CONECT   34   27   33   35                                                  
CONECT   35   24   34                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Value	Source
Isosilybin	MeSH

Chemical Formula

C₂₅H₂₂O₁₀

Average Mass

482.4362 Da

Monoisotopic Mass

482.12130 Da

IUPAC Name

3,5,7-trihydroxy-2-[2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

3,5,7-trihydroxy-2-[2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC=C1O)C1OC2=C(OC1CO)C=C(C=C2)C1OC2=C(C(O)=CC(O)=C2)C(=O)C1O

InChI Identifier

InChI=1S/C25H22O10/c1-32-17-6-11(2-4-14(17)28)24-20(10-26)33-18-7-12(3-5-16(18)34-24)25-23(31)22(30)21-15(29)8-13(27)9-19(21)35-25/h2-9,20,23-29,31H,10H2,1H3

InChI Key

FDQAOULAVFHKBX-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
Anastatica hierochuntica	LOTUS Database	35616633
Silybum marianum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonolignans. These are non-conventional lignans that derived from flavonoids. They are characterized by a p-dioxin ring substituted at one carbon atom by a C3C6 (phenylpropan) group and fused to the B-ring of the 2-phenylchromene moiety.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Flavonolignans

Sub Class

Not Available

Direct Parent

Flavonolignans

Alternative Parents

Substituents

Flavonolignan
Hydroxyflavonoid
3-hydroxyflavonoid
Flavanonol
Flavanone
7-hydroxyflavonoid
5-hydroxyflavonoid
Flavan
Phenylbenzodioxane
2-phenylbenzo-1,4-dioxane
Chromone
1-benzopyran
Methoxyphenol
Benzopyran
Chromane
Benzodioxane
Benzo-1,4-dioxane
Phenoxy compound
Anisole
Methoxybenzene
Aryl alkyl ketone
Aryl ketone
Phenol ether
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Para-dioxin
Monocyclic benzene moiety
Vinylogous acid
Secondary alcohol
Ketone
Polyol
Organoheterocyclic compound
Ether
Oxacycle
Alcohol
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary 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	2.35	ALOGPS
logP	2.63	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	7.81	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.14 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	120.29 m³·mol⁻¹	ChemAxon
Polarizability	48.51 Å³	ChemAxon
Number of Rings	5	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

HMDB0033322

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3085830

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Deep G, Oberlies NH, Kroll DJ, Agarwal R: Isosilybin B and isosilybin A inhibit growth, induce G1 arrest and cause apoptosis in human prostate cancer LNCaP and 22Rv1 cells. Carcinogenesis. 2007 Jul;28(7):1533-42. doi: 10.1093/carcin/bgm069. Epub 2007 Mar 26. [PubMed:17389612 ]
Deep G, Oberlies NH, Kroll DJ, Agarwal R: Isosilybin B causes androgen receptor degradation in human prostate carcinoma cells via PI3K-Akt-Mdm2-mediated pathway. Oncogene. 2008 Jun 26;27(28):3986-98. doi: 10.1038/onc.2008.45. Epub 2008 Mar 10. [PubMed:18332867 ]
Deep G, Gangar SC, Oberlies NH, Kroll DJ, Agarwal R: Isosilybin A induces apoptosis in human prostate cancer cells via targeting Akt, NF-kappaB, and androgen receptor signaling. Mol Carcinog. 2010 Oct;49(10):902-12. doi: 10.1002/mc.20670. [PubMed:20721970 ]

Showing NP-Card for Isosilybin (NP0136995)

MOL for NP0136995 (Isosilybin)

3D MOL for NP0136995 (Isosilybin)

3D SDF for NP0136995 (Isosilybin)

3D-SDF for NP0136995 (Isosilybin)

PDB for NP0136995 (Isosilybin)

3D PDB for NP0136995 (Isosilybin)

SMILES for NP0136995 (Isosilybin)

INCHI for NP0136995 (Isosilybin)

Structure for NP0136995 (Isosilybin)

3D Structure for NP0136995 (Isosilybin)