NP-MRD: Showing NP-Card for Davidigenin (NP0055290)

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Record Information

Version

2.0

Created at

2022-04-28 01:23:49 UTC

Updated at

2022-04-28 01:23:49 UTC

NP-MRD ID

NP0055290

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Davidigenin

Description

Davidigenin belongs to the class of organic compounds known as 2'-hydroxy-dihydrochalcones. These are organic compounds containing dihydrochalcone skeleton that carries a hydroxyl group at the 2'-position. Thus, davidigenin is considered to be a flavonoid lipid molecule. Davidigenin is found in Artemisia dracunculus, Fadogia ancylantha, Mascarenhasia arborescens and Viburnum davidii. Davidigenin was first documented in 2000 (PMID: 10705748). Davidigenin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 11105563) (PMID: 20580662) (PMID: 21798321).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
    0.0449    1.4520   -0.1818 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6524    0.3977   -0.4435 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0066   -0.6987   -1.1716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3775   -0.4768   -1.6441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4071   -0.1892   -0.6582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0428   -1.1638    0.0939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0357   -0.8640    0.9957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4463    0.4326    1.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4453    0.7569    2.0977 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8399    1.4296    0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8299    1.1025   -0.4499 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0502    0.2946    0.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6046    1.3626    0.7102 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9022    1.2503    1.1323 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6904    0.1548    0.9091 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0211    0.0916    1.3664 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1262   -0.8889    0.2154 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8063   -0.8197   -0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3296   -1.9146   -0.9230 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1152   -1.6357   -0.5682 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6367   -0.8693   -2.0960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7248   -1.3162   -2.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3366    0.3972   -2.3657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7319   -2.1847   -0.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5117   -1.6689    1.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7437    1.7051    2.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1526    2.4546    0.6096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4033    1.9265   -1.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9841    2.2239    0.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3234    2.0762    1.6720 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1427   -0.2951    2.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7159   -1.7809    0.0145 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8765   -2.7424   -1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 12  1  0
 12 18  2  0
 18 19  1  0
 18 17  1  0
 17 15  2  0
 15 16  1  0
 15 14  1  0
 14 13  2  0
  5 11  1  0
 11 10  2  0
 10  8  1  0
 13 12  1  0
  9 26  1  0
  7 25  1  0
  6 24  1  0
  4 22  1  0
  4 23  1  0
  3 20  1  0
  3 21  1  0
 19 33  1  0
 17 32  1  0
 16 31  1  0
 14 30  1  0
 13 29  1  0
 11 28  1  0
 10 27  1  0
M  END


  Mrv1652310051715232D          

 19 20  0  0  0  0            999 V2000
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  7  6  2  0  0  0  0
  8  3  1  0  0  0  0
 10  1  2  0  0  0  0
 10  2  1  0  0  0  0
 10  3  1  0  0  0  0
 11  4  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 12  9  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  1  0  0  0  0
 15 13  2  0  0  0  0
 16 11  1  0  0  0  0
 17 12  1  0  0  0  0
 18 14  2  0  0  0  0
 19 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0055290

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=C(CCC(=O)C2=C(O)C=C(O)C=C2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O4/c16-11-4-1-10(2-5-11)3-8-14(18)13-7-6-12(17)9-15(13)19/h1-2,4-7,9,16-17,19H,3,8H2

> <INCHI_KEY>
UDGKKUWYNITJRX-UHFFFAOYSA-N

> <FORMULA>
C15H14O4

> <MOLECULAR_WEIGHT>
258.273

> <EXACT_MASS>
258.089208931

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
27.067623511597844

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2,4-dihydroxyphenyl)-3-(4-hydroxyphenyl)propan-1-one

> <ALOGPS_LOGP>
2.77

> <JCHEM_LOGP>
3.549105854333334

> <ALOGPS_LOGS>
-3.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.349755040242568

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.855788071973414

> <JCHEM_PKA_STRONGEST_BASIC>
-4.908504640676328

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
71.7264

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.72e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
davidigenin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-OCT-17         0                                  
HETATM    1  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
CONECT    1    4   10                                                       
CONECT    2    5   10                                                       
CONECT    3    8   10                                                       
CONECT    4    1   11                                                       
CONECT    5    2   11                                                       
CONECT    6    7   12                                                       
CONECT    7    6   13                                                       
CONECT    8    3   14                                                       
CONECT    9   12   15                                                       
CONECT   10    1    2    3                                                  
CONECT   11    4    5   16                                                  
CONECT   12    6    9   17                                                  
CONECT   13    7   14   15                                                  
CONECT   14    8   13   18                                                  
CONECT   15    9   13   19                                                  
CONECT   16   11                                                            
CONECT   17   12                                                            
CONECT   18   14                                                            
CONECT   19   15                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Value	Source
4,2',4'-Trihydroxydihydrochalcone	ChEBI

Chemical Formula

C₁₅H₁₄O₄

Average Mass

258.2730 Da

Monoisotopic Mass

258.08921 Da

IUPAC Name

1-(2,4-dihydroxyphenyl)-3-(4-hydroxyphenyl)propan-1-one

Traditional Name

davidigenin

CAS Registry Number

Not Available

SMILES

OC1=CC=C(CCC(=O)C2=C(O)C=C(O)C=C2)C=C1

InChI Identifier

InChI=1S/C15H14O4/c16-11-4-1-10(2-5-11)3-8-14(18)13-7-6-12(17)9-15(13)19/h1-2,4-7,9,16-17,19H,3,8H2

InChI Key

UDGKKUWYNITJRX-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, 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
Artemisia dracunculus	LOTUS Database	35616633
Fadogia ancylantha	LOTUS Database	35616633
Mascarenhasia arborescens	LOTUS Database	35616633
Viburnum davidii	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2'-hydroxy-dihydrochalcones. These are organic compounds containing dihydrochalcone skeleton that carries a hydroxyl group at the 2'-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Linear 1,3-diarylpropanoids

Sub Class

Chalcones and dihydrochalcones

Direct Parent

2'-Hydroxy-dihydrochalcones

Alternative Parents

Substituents

2'-hydroxy-dihydrochalcone
Cinnamylphenol
Alkyl-phenylketone
Butyrophenone
Phenylketone
Benzoyl
Resorcinol
Aryl alkyl ketone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Vinylogous acid
Ketone
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

polyphenol (CHEBI:27655 )
dihydrochalcones (CHEBI:27655 )
dihydrochalcones (C09618 )
Chalcones and dihydrochalcones (C09618 )
Chalcones and dihydrochalcones (LMPK12120452 )

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	2.77	ALOGPS
logP	3.55	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	7.86	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	71.73 m³·mol⁻¹	ChemAxon
Polarizability	27.07 Å³	ChemAxon
Number of Rings	2	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

HMDB0151846

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00007926

Chemspider ID

Not Available

KEGG Compound ID

C09618

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

27655

Good Scents ID

Not Available

References

General References

Homma M, Minami M, Taniguchi C, Oka K, Morita S, Niitsuma T, Hayashi T: Inhibitory effects of lignans and flavonoids in saiboku-to, a herbal medicine for bronchial asthma, on the release of leukotrienes from human polymorphonuclear leukocytes. Planta Med. 2000 Feb;66(1):88-91. doi: 10.1055/s-0029-1243120. [PubMed:10705748 ]
Taniguchi C, Homma M, Takano O, Hirano T, Oka K, Aoyagi Y, Niitsuma T, Hayashi T: Pharmacological effects of urinary products obtained after treatment with saiboku-to, a herbal medicine for bronchial asthma, on type IV allergic reaction. Planta Med. 2000 Oct;66(7):607-11. doi: 10.1055/s-2000-8626. [PubMed:11105563 ]
Desire O, Riviere C, Razafindrazaka R, Goossens L, Moreau S, Guillon J, Uverg-Ratsimamanga S, Andriamadio P, Moore N, Randriantsoa A, Raharisololalao A: Antispasmodic and antioxidant activities of fractions and bioactive constituent davidigenin isolated from Mascarenhasia arborescens. J Ethnopharmacol. 2010 Jul 20;130(2):320-8. doi: 10.1016/j.jep.2010.05.017. Epub 2010 May 16. [PubMed:20580662 ]
Eisenman SW, Poulev A, Struwe L, Raskin I, Ribnicky DM: Qualitative variation of anti-diabetic compounds in different tarragon (Artemisia dracunculus L.) cytotypes. Fitoterapia. 2011 Oct;82(7):1062-74. doi: 10.1016/j.fitote.2011.07.003. Epub 2011 Jul 21. [PubMed:21798321 ]

Showing NP-Card for Davidigenin (NP0055290)

MOL for NP0055290 (Davidigenin)

3D MOL for NP0055290 (Davidigenin)

3D SDF for NP0055290 (Davidigenin)

3D-SDF for NP0055290 (Davidigenin)

PDB for NP0055290 (Davidigenin)

3D PDB for NP0055290 (Davidigenin)

SMILES for NP0055290 (Davidigenin)

INCHI for NP0055290 (Davidigenin)

Structure for NP0055290 (Davidigenin)

3D Structure for NP0055290 (Davidigenin)