NP-MRD: Showing NP-Card for Prunetin (NP0047863)

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Record Information

Version

2.0

Created at

2022-03-17 20:47:11 UTC

Updated at

2024-09-03 04:17:08 UTC

NP-MRD ID

NP0047863

Natural Product DOI

https://doi.org/10.57994/0928

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Prunetin

Description

Prunetin, also known as padmakastein, belongs to the class of organic compounds known as 7-o-methylisoflavones. These are isoflavones with methoxy groups attached to the C7 atom of the isoflavone backbone. Thus, prunetin is considered to be a flavonoid lipid molecule. Prunetin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Prunetin is a bitter tasting compound. Outside of the human body, Prunetin has been detected, but not quantified in, several different foods, such as herbs and spices, prunus (cherry, plum), sour cherries, and tea. This could make prunetin a potential biomarker for the consumption of these foods. Prunetin is found in Achlys triphylla, Andira inermis, Andira surinamensis, Butea monosperma, Cladrastis platycarpa, Crotalaria lachnophora, Dalbergia miscolobium, Dalbergia odorifera , Dalbergia sissoo, Dalbergia violacea, Dermatophyllum secundiflorum, Derris laxiflora, Ficus nervosa, Flemingia macrophylla, Genista carinalis, Glycyrrhiza glabra , Glycyrrhiza pallidiflora, Iris milesii, Millettia erythrocalyx, Myristica malabarica , Occurs in several, Ochna calodendron, Oroxylum indicum , Pisum sativum, Prunus cerasoides, Prunus nipponica, Prunus puddum , Prunus puddun, Prunus spp. , Prunus verecunda, Pterocarpus angolensis , Pterocarpus soyauxii, Pueraria montana, Pycnanthus angolensis, Sophora secundiflora , Streptomyces sp. M491, Sophora japonica , Taxus chinensis and Trifolium pratense . Prunetin was first documented in 1949 (PMID: 15408466). A hydroxyisoflavone that is genistein in which the hydroxy group at position 7 is replaced by a methoxy group (PMID: 22148193) (PMID: 21305630) (PMID: 22010824) (PMID: 23265084).

Structure

MOL SDF PDB SMILES InChI

Prunetin
  Mrv1652305062021512D          

 21 23  0  0  0  0            999 V2000
   10.7820   -6.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7820   -6.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0675   -5.6969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4965   -5.6969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4965   -7.3468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0675   -7.3468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3531   -6.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2109   -6.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2109   -6.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4965   -8.1719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3531   -6.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0675   -8.1719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9254   -7.3468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6398   -6.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9254   -8.1719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3543   -7.3468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6398   -8.5844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3543   -8.1719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0688   -8.5844    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6386   -5.6969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9241   -6.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  6 12  1  0  0  0  0
  7 20  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 15 17  2  0  0  0  0
 16 18  2  0  0  0  0
 18 19  1  0  0  0  0
  7 11  1  0  0  0  0
  8  9  2  0  0  0  0
 17 18  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047863

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC2=C(C(O)=C1)C(=O)C(=CO2)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H12O5/c1-20-11-6-13(18)15-14(7-11)21-8-12(16(15)19)9-2-4-10(17)5-3-9/h2-8,17-18H,1H3

> <INCHI_KEY>
KQMVAGISDHMXJJ-UHFFFAOYSA-N

> <FORMULA>
C16H12O5

> <MOLECULAR_WEIGHT>
284.267

> <EXACT_MASS>
284.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
28.70535120292798

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-3-(4-hydroxyphenyl)-7-methoxy-4H-chromen-4-one

> <ALOGPS_LOGP>
3.36

> <JCHEM_LOGP>
3.2227664456666663

> <ALOGPS_LOGS>
-3.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.974426058464246

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.323399360483996

> <JCHEM_PKA_STRONGEST_BASIC>
-4.737551646594349

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
76.1652

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.86e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
prunetin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Prunetin                                          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-20         0                                  
HETATM    1  C   UNK     0      20.126 -11.404   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.126 -12.944   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.793 -10.634   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      21.460 -10.634   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      21.460 -13.714   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.793 -13.714   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.459 -11.404   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.794 -11.404   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      22.794 -12.944   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      21.460 -15.254   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      17.459 -12.944   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      18.793 -15.254   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      24.127 -13.714   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      25.461 -12.944   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      24.127 -15.254   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      26.795 -13.714   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      25.461 -16.024   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      26.795 -15.254   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      28.128 -16.024   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      16.125 -10.634   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      14.792 -11.404   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9   10                                                  
CONECT    6    2   11   12                                                  
CONECT    7    3   20   11                                                  
CONECT    8    4    9                                                       
CONECT    9    5   13    8                                                  
CONECT   10    5                                                            
CONECT   11    6    7                                                       
CONECT   12    6                                                            
CONECT   13    9   14   15                                                  
CONECT   14   13   16                                                       
CONECT   15   13   17                                                       
CONECT   16   14   18                                                       
CONECT   17   15   18                                                       
CONECT   18   16   19   17                                                  
CONECT   19   18                                                            
CONECT   20    7   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
4',5-Dihydroxy-7-methoxygenistein	ChEBI
4',5-Dihydroxy-7-methoxyisoflavone	ChEBI
5-Hydroxy-3-(4-hydroxyphenyl)-7-methoxy-4-benzopyrone	ChEBI
5-Hydroxy-3-(4-hydroxyphenyl)-7-methoxy-4H-1-benzopyran-4-one	ChEBI
7-O-Methyl-genistein	ChEBI
Padmakastein	ChEBI
Prunusetin	ChEBI
5,4'-Dihydroxy-7-methoxyisoflavone	HMDB
5-Hydroxy-3-(4-hydroxyphenyl)-7-methoxy-4H-1-benzopyran-4-one, 9ci	HMDB
5-Hydroxy-3-(4-hydroxyphenyl)-7-methoxy-4H-chromen-4-one	HMDB
Isoflavone, 4',5-dihydroxy-7-methoxy- (7ci,8ci)	HMDB

Chemical Formula

C₁₆H₁₂O₅

Average Mass

284.2670 Da

Monoisotopic Mass

284.06847 Da

IUPAC Name

5-hydroxy-3-(4-hydroxyphenyl)-7-methoxy-4H-chromen-4-one

Traditional Name

prunetin

CAS Registry Number

552-59-0

SMILES

COC1=CC2=C(C(O)=C1)C(=O)C(=CO2)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C16H12O5/c1-20-11-6-13(18)15-14(7-11)21-8-12(16(15)19)9-2-4-10(17)5-3-9/h2-8,17-18H,1H3

InChI Key

KQMVAGISDHMXJJ-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2023-09-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2023-09-13	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Achlys triphylla	LOTUS Database	35616633
Andira inermis	LOTUS Database	35616633
Andira surinamensis	LOTUS Database	35616633
Butea monosperma	LOTUS Database	35616633
Cladrastis platycarpa	LOTUS Database	35616633
Crotalaria lachnophora	LOTUS Database	35616633
Dalbergia miscolobium	Plant	KNApSAcK
Dalbergia odorifera	Plant	KNApSAcK
Dalbergia sissoo	LOTUS Database	35616633
Dalbergia violacea	Plant	KNApSAcK
Dermatophyllum secundiflorum	LOTUS Database	35616633
Derris laxiflora	LOTUS Database	35616633
Ficus nervosa	LOTUS Database	35616633
Flemingia macrophylla	LOTUS Database	35616633
Genista carinalis	Plant	KNApSAcK
Glycyrrhiza glabra	Plant	KNApSAcK
Glycyrrhiza pallidiflora	LOTUS Database	35616633
Iris milesii	LOTUS Database	35616633
Millettia erythrocalyx	LOTUS Database	35616633
Myristica malabarica	Plant	KNApSAcK
Occurs in several	-	KNApSAcK
Ochna calodendron	Plant	KNApSAcK
Oroxylum indicum	Plant	KNApSAcK
Pisum sativum	LOTUS Database	35616633
Prunus avium L.	FooDB	KNAPSACK
Prunus cerasoides	LOTUS Database	35616633
Prunus cerasus	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Prunus nipponica	LOTUS Database	35616633
Prunus puddum	Plant	KNApSAcK
Prunus puddun	Plant	KNApSAcK
Prunus spp.	Plant	KNApSAcK
Prunus verecunda	Plant	KNApSAcK
Pterocarpus angolensis	Plant	KNApSAcK
Pterocarpus soyauxii	LOTUS Database	35616633
Pueraria montana	LOTUS Database	35616633
Pycnanthus angolensis	LOTUS Database	35616633
Sophora secundiflora	Plant	KNApSAcK
Streptomyces sp. M491	Bacteria	KNApSAcK
Styphnolobium japonicum	Plant	KNApSAcK
Taxus chinensis	Plant	KNApSAcK
Trifolium pratense	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 7-o-methylisoflavones. These are isoflavones with methoxy groups attached to the C7 atom of the isoflavone backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

O-methylated isoflavonoids

Direct Parent

7-O-methylisoflavones

Alternative Parents

Substituents

7-o-methylisoflavone
Hydroxyisoflavonoid
Isoflavone
Chromone
Benzopyran
1-benzopyran
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Monocyclic benzene moiety
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Organoheterocyclic compound
Ether
Oxacycle
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

hydroxyisoflavone (CHEBI:8600 )
methoxyisoflavone (CHEBI:8600 )
isoflavones (C10521 )
Isoflavonoids (C10521 )
Isoflavonoids (LMPK12050353 )
a small molecule (CPD-3521 )

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	3.36	ALOGPS
logP	3.22	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	7.32	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	76.17 m³·mol⁻¹	ChemAxon
Polarizability	28.71 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0034127

DrugBank ID

Not Available

Phenol Explorer Compound ID

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Prunetin

METLIN ID

Not Available

PubChem Compound

5281804

PDB ID

Not Available

ChEBI ID

8600

Good Scents ID

Not Available

References

General References

Wong SL, Chang HS, Wang GJ, Chiang MY, Huang HY, Chen CH, Tsai SC, Lin CH, Chen IS: Secondary metabolites from the roots of Neolitsea daibuensis and their anti-inflammatory activity. J Nat Prod. 2011 Dec 27;74(12):2489-96. doi: 10.1021/np100874f. Epub 2011 Dec 7. [PubMed:22148193 ]
IYER RN, SHAH KH, VENKATARAMAN K: A synthesis of prunetin. Curr Sci. 1949 Nov;18(11):404-6. [PubMed:15408466 ]
Lee HJ, Lee SY, Lee MN, Kim JH, Chang GT, Seok JH, Lee CJ: Inhibition of secretion, production and gene expression of mucin from cultured airway epithelial cells by prunetin. Phytother Res. 2011 Aug;25(8):1196-200. doi: 10.1002/ptr.3362. Epub 2011 Feb 9. [PubMed:21305630 ]
Sekine R, Vongsvivut J, Robertson EG, Spiccia L, McNaughton D: Analysis of 5-hydroxyisoflavones by surface-enhanced Raman spectroscopy: genistein and methoxy derivatives. J Phys Chem B. 2011 Dec 1;115(47):13943-54. doi: 10.1021/jp207730g. Epub 2011 Nov 7. [PubMed:22010824 ]
Bae M, Woo M, Kusuma IW, Arung ET, Yang CH, Kim YU: Inhibitory effects of isoflavonoids on rat prostate testosterone 5alpha-reductase. J Acupunct Meridian Stud. 2012 Dec;5(6):319-22. doi: 10.1016/j.jams.2012.07.022. Epub 2012 Aug 9. [PubMed:23265084 ]

Showing NP-Card for Prunetin (NP0047863)

MOL for NP0047863 (Prunetin)

3D MOL for NP0047863 (Prunetin)

3D SDF for NP0047863 (Prunetin)

3D-SDF for NP0047863 (Prunetin)

PDB for NP0047863 (Prunetin)

3D PDB for NP0047863 (Prunetin)

SMILES for NP0047863 (Prunetin)

INCHI for NP0047863 (Prunetin)

Structure for NP0047863 (Prunetin)

3D Structure for NP0047863 (Prunetin)