NP-MRD: Showing NP-Card for 4-Demethyl-3,9-dihydroeucomin (NP0138396)

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Record Information

Version

1.0

Created at

2022-05-31 17:57:41 UTC

Updated at

2022-05-31 17:57:41 UTC

NP-MRD ID

NP0138396

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-Demethyl-3,9-dihydroeucomin

Description

(-)-5,7-Dihydroxy-3-(4-hydroxybenzyl)-4-chromanone belongs to the class of organic compounds known as homoisoflavanones. These are homoisoflavonoids with a structure based on the chromanone system. Chromanone is a bicyclic compound consisting of a 3,4-dihydro-1-benzopyran, which bears a ketone group at the 4-position (-)-5,7-Dihydroxy-3-(4-hydroxybenzyl)-4-chromanone is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (-)-5,7-Dihydroxy-3-(4-hydroxybenzyl)-4-chromanone has been detected, but not quantified in, herbs and spices. 4-Demethyl-3,9-dihydroeucomin is found in Dracaena draco, Ledebouria floribunda, Leopoldia comosa, Muscari neglectum and Soymida febrifuga. This could make (-)-5,7-dihydroxy-3-(4-hydroxybenzyl)-4-chromanone a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 37  0  0  0  0  0  0  0  0999 V2000
   -1.2110    1.5150    1.8461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    0.8069    0.8209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4381    0.3190    0.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6538    0.8261    0.7082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5903    1.8172    1.6848 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8628    0.3747    0.2006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8349   -0.6156   -0.7704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0567   -1.0582   -1.2700 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6224   -1.1166   -1.1980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4254   -0.6797   -0.7054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1917   -1.1649   -1.1163 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0652   -1.0301   -0.2664 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0635    0.4150    0.1007 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2181    0.7051    1.0127 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5257    0.3486    0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0446   -0.9118    0.6790 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2914   -1.2814    0.1681 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0402   -0.3886   -0.5685 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2824   -0.7502   -1.0800 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5169    0.8700   -0.7796 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2723    1.2317   -0.2668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4089    2.2614    2.0776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7746    0.8048    0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4539   -0.5829   -2.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6400   -1.8876   -1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8339   -1.4346   -0.7713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2952   -1.6036    0.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1202    0.9931   -0.8545 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0330    0.1707    1.9648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1737    1.7909    1.2614 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4749   -1.6389    1.2579 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7032   -2.2670    0.3324 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1516   -0.6341   -0.6041 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0881    1.5841   -1.3542 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8686    2.2114   -0.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 18  1  0
 18 17  2  0
 17 16  1  0
 16 15  2  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  2  0
  9  7  1  0
  7  8  1  0
  7  6  2  0
  6  4  1  0
  4  5  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
 15 21  1  0
 21 20  2  0
 20 18  1  0
  2 13  1  0
  3 10  1  0
 19 33  1  0
 17 32  1  0
 16 31  1  0
 14 29  1  0
 14 30  1  0
 13 28  1  6
 12 26  1  0
 12 27  1  0
  9 25  1  0
  8 24  1  0
  6 23  1  0
  5 22  1  0
 21 35  1  0
 20 34  1  0
M  END


  Mrv0541 05061310282D          

 21 23  0  0  0  0            999 V2000
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    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
    6.4302    2.0625    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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    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
    7.1447    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  9  1  2  0  0  0  0
  9  2  1  0  0  0  0
  9  5  1  0  0  0  0
 10  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  3  2  0  0  0  0
 11  4  1  0  0  0  0
 12  6  2  0  0  0  0
 12  7  1  0  0  0  0
 13  6  1  0  0  0  0
 14  7  2  0  0  0  0
 15 13  2  0  0  0  0
 15 14  1  0  0  0  0
 16 10  1  0  0  0  0
 16 15  1  0  0  0  0
 17 11  1  0  0  0  0
 18 12  1  0  0  0  0
 19 13  1  0  0  0  0
 20 16  2  0  0  0  0
 21  8  1  0  0  0  0
 21 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138396

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=C(CC2COC3=CC(O)=CC(O)=C3C2=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H14O5/c17-11-3-1-9(2-4-11)5-10-8-21-14-7-12(18)6-13(19)15(14)16(10)20/h1-4,6-7,10,17-19H,5,8H2

> <INCHI_KEY>
FIASLUPJXGTCKM-UHFFFAOYSA-N

> <FORMULA>
C16H14O5

> <MOLECULAR_WEIGHT>
286.2794

> <EXACT_MASS>
286.084123558

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
28.37544250507686

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,7-dihydroxy-3-[(4-hydroxyphenyl)methyl]-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.61

> <JCHEM_LOGP>
3.1722267789999994

> <ALOGPS_LOGS>
-3.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.486255759802932

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.910216475688456

> <JCHEM_PKA_STRONGEST_BASIC>
-3.862547305038265

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
76.2775

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-3-[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      13.337   1.540   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
CONECT    1    3    9                                                       
CONECT    2    4    9                                                       
CONECT    3    1   11                                                       
CONECT    4    2   11                                                       
CONECT    5    9   10                                                       
CONECT    6   12   13                                                       
CONECT    7   12   14                                                       
CONECT    8   10   21                                                       
CONECT    9    1    2    5                                                  
CONECT   10    5    8   16                                                  
CONECT   11    3    4   17                                                  
CONECT   12    6    7   18                                                  
CONECT   13    6   15   19                                                  
CONECT   14    7   15   21                                                  
CONECT   15   13   14   16                                                  
CONECT   16   10   15   20                                                  
CONECT   17   11                                                            
CONECT   18   12                                                            
CONECT   19   13                                                            
CONECT   20   16                                                            
CONECT   21    8   14                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₄O₅

Average Mass

286.2794 Da

Monoisotopic Mass

286.08412 Da

IUPAC Name

5,7-dihydroxy-3-[(4-hydroxyphenyl)methyl]-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

5,7-dihydroxy-3-[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

107585-77-3

SMILES

OC1=CC=C(CC2COC3=CC(O)=CC(O)=C3C2=O)C=C1

InChI Identifier

InChI=1S/C16H14O5/c17-11-3-1-9(2-4-11)5-10-8-21-14-7-12(18)6-13(19)15(14)16(10)20/h1-4,6-7,10,17-19H,5,8H2

InChI Key

FIASLUPJXGTCKM-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
Dracaena draco	LOTUS Database	35616633
Ledebouria floribunda	LOTUS Database	35616633
Muscari comosum	LOTUS Database	35616633
Muscari neglectum	LOTUS Database	35616633
Soymida febrifuga	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as homoisoflavanones. These are homoisoflavonoids with a structure based on the chromanone system. Chromanone is a bicyclic compound consisting of a 3,4-dihydro-1-benzopyran, which bears a ketone group at the 4-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Homoisoflavonoids

Sub Class

Homoisoflavans

Direct Parent

Homoisoflavanones

Alternative Parents

Substituents

Homoisoflavanone
Chromone
Chromane
Benzopyran
1-benzopyran
Aryl alkyl ketone
Aryl ketone
Phenol
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Vinylogous acid
Ketone
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
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	2.61	ALOGPS
logP	3.17	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	7.91	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	76.28 m³·mol⁻¹	ChemAxon
Polarizability	28.38 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

HMDB0038448

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017806

KNApSAcK ID

Not Available

Chemspider ID

8146810

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9971218

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 4-Demethyl-3,9-dihydroeucomin (NP0138396)

MOL for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

3D MOL for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

3D SDF for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

3D-SDF for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

PDB for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

3D PDB for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

SMILES for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

INCHI for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

Structure for NP0138396 (4-Demethyl-3,9-dihydroeucomin)

3D Structure for NP0138396 (4-Demethyl-3,9-dihydroeucomin)