NP-MRD: Showing NP-Card for 3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one (NP0238468)

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Record Information

Version

2.0

Created at

2022-09-06 21:52:11 UTC

Updated at

2022-09-06 21:52:11 UTC

NP-MRD ID

NP0238468

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one

Description

3,5,7-Trihydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one belongs to the class of organic compounds known as flavonols. Flavonols are compounds that contain a flavone (2-phenyl-1-benzopyran-4-one) backbone carrying a hydroxyl group at the 3-position. 3,5,7-Trihydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one is an extremely weak basic (essentially neutral) compound (based on its pKa). 3,5,7-Trihydroxy-2-(3-hydroxyphenyl)-4h-chromen-4-one is a predicted metabolite generated by BioTransformer¹ that is produced by the metabolism of 2-(3,5-dihydroxyphenyl)-3,5,7-trihydroxy-4h-chromen-4-one. It is generated by Dehydroxylase enzyme via a resorcinol-m-dehydroxylation reaction. 3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one is found in Costus spicatus. This resorcinol-m-dehydroxylation occurs in human gut microbiota.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
    1.9517    2.9180   -0.2797 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4529    1.7855   -0.2030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0482    1.6956   -0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6788    2.8716   -0.1651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5476    0.4721   -0.0534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9867    0.2883    0.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9234    1.2764    0.0088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2914    1.0575    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7466   -0.2183    0.1596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8291   -1.2634    0.1715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3552   -2.5510    0.2568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4796   -1.0227    0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2164   -0.6249   -0.0324 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5120   -0.5933   -0.0893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2259   -1.8056   -0.0606 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5920   -1.8147   -0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3123   -3.0328   -0.0897 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2375   -0.6168   -0.2046 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5464    0.6158   -0.2353 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2617    1.7688   -0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1706    0.6223   -0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2519    3.7800   -0.2277 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6409    2.3166   -0.0541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9513    1.9088    0.0645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8143   -0.3938    0.2138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7847   -3.3848    0.2732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8164   -1.8779    0.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6897   -2.7391    0.0079 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5446   -3.5278   -0.9223 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3316   -0.5943   -0.2524 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0043    2.6839   -0.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  9  2  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6 12  2  0
  6  5  1  0
  5  3  2  0
  3  4  1  0
  3  2  1  0
  2  1  2  0
  2 21  1  0
 21 19  2  0
 19 20  1  0
 19 18  1  0
 18 16  2  0
 16 17  1  0
 16 15  1  0
 15 14  2  0
 14 13  1  0
 12 10  1  0
 13  5  1  0
 14 21  1  0
 11 26  1  0
  9 25  1  0
  8 24  1  0
  7 23  1  0
 12 27  1  0
  4 22  1  0
 20 31  1  0
 18 30  1  0
 17 29  1  0
 15 28  1  0
M  END


  Mrv1652308171916572D          

 21 23  0  0  0  0            999 V2000
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    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
    3.5724   -0.4125    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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   -1.6500    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   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    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
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  7  2  1  0  0  0  0
  7  4  2  0  0  0  0
  8  3  2  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
  9  6  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  2  0  0  0  0
 12 10  2  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15  7  1  0  0  0  0
 15 14  2  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 19 13  2  0  0  0  0
 20 14  1  0  0  0  0
 21 11  1  0  0  0  0
 21 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0238468

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=CC(=C1)C1=C(O)C(=O)C2=C(O)C=C(O)C=C2O1

> <INCHI_IDENTIFIER>
InChI=1S/C15H10O6/c16-8-3-1-2-7(4-8)15-14(20)13(19)12-10(18)5-9(17)6-11(12)21-15/h1-6,16-18,20H

> <INCHI_KEY>
ABDQTIKKAYGHNV-UHFFFAOYSA-N

> <FORMULA>
C15H10O6

> <MOLECULAR_WEIGHT>
286.239

> <EXACT_MASS>
286.047738042

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
27.520732159051256

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,5,7-trihydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one

> <ALOGPS_LOGP>
1.94

> <JCHEM_LOGP>
2.4598647856666664

> <ALOGPS_LOGS>
-3.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.910659826270707

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.381357047916055

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9595062694392444

> <JCHEM_POLAR_SURFACE_AREA>
107.22

> <JCHEM_REFRACTIVITY>
74.88130000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.94e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-AUG-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-AUG-19         0                                  
HETATM    1  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   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  -3.080   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  -0.770   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    7                                                       
CONECT    3    1    8                                                       
CONECT    4    7    8                                                       
CONECT    5    9   10                                                       
CONECT    6    9   11                                                       
CONECT    7    2    4   15                                                  
CONECT    8    3    4   16                                                  
CONECT    9    5    6   17                                                  
CONECT   10    5   12   18                                                  
CONECT   11    6   12   21                                                  
CONECT   12   10   11   13                                                  
CONECT   13   12   14   19                                                  
CONECT   14   13   15   20                                                  
CONECT   15    7   14   21                                                  
CONECT   16    8                                                            
CONECT   17    9                                                            
CONECT   18   10                                                            
CONECT   19   13                                                            
CONECT   20   14                                                            
CONECT   21   11   15                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₀O₆

Average Mass

286.2390 Da

Monoisotopic Mass

286.04774 Da

IUPAC Name

3,5,7-trihydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one

Traditional Name

3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one

CAS Registry Number

Not Available

SMILES

OC1=CC=CC(=C1)C1=C(O)C(=O)C2=C(O)C=C(O)C=C2O1

InChI Identifier

InChI=1S/C15H10O6/c16-8-3-1-2-7(4-8)15-14(20)13(19)12-10(18)5-9(17)6-11(12)21-15/h1-6,16-18,20H

InChI Key

ABDQTIKKAYGHNV-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
Costus spicatus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonols. Flavonols are compounds that contain a flavone (2-phenyl-1-benzopyran-4-one) backbone carrying a hydroxyl group at the 3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavones

Direct Parent

Flavonols

Alternative Parents

Substituents

3-hydroxyflavone
3'-hydroxyflavonoid
3-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Chromone
Benzopyran
1-benzopyran
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Monocyclic benzene moiety
Pyran
Benzenoid
Heteroaromatic compound
Vinylogous acid
Polyol
Organoheterocyclic compound
Oxacycle
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	1.94	ALOGPS
logP	2.46	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	6.38	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	107.22 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	74.88 m³·mol⁻¹	ChemAxon
Polarizability	27.52 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

HMDB0125209

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8036358

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9860659

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one (NP0238468)

MOL for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

3D MOL for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

3D SDF for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

3D-SDF for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

PDB for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

3D PDB for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

SMILES for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

INCHI for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

Structure for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)

3D Structure for NP0238468 (3,5,7-trihydroxy-2-(3-hydroxyphenyl)chromen-4-one)