NP-MRD: Showing NP-Card for 5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one (NP0258098)

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Record Information

Version

2.0

Created at

2022-09-07 23:24:29 UTC

Updated at

2022-09-07 23:24:29 UTC

NP-MRD ID

NP0258098

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one

Description

5,7-Dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)-4H-chromen-4-one belongs to the class of organic compounds known as depsides and depsidones. These are polycyclic compounds that is either a polyphenolic compound composed of two or more monocyclic aromatic units linked by an ester bond (depside), or a compound containing the depsidone structure (depsidone). 5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one is found in Artabotrys hexapetalus. 5,7-Dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)-4H-chromen-4-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171510182D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004171510182D          

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   -3.4629   -3.5541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2475   -3.2992    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2913   -4.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9044   -4.9131    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 18 25  1  0  0  0  0
 25 26  1  0  0  0  0
 15 26  1  0  0  0  0
 26 27  2  0  0  0  0
 16 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 28 34  1  0  0  0  0
  4 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  1  0  0  0  0
  2 39  1  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0258098

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(OC2C(OC3=C(OC4=CC(O)=CC(O)=C4C3=O)C3=CC=C(O)C=C3)OC(CO)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O14/c1-9-17(31)20(34)21(35)25(36-9)40-24-18(32)15(8-27)38-26(24)39-23-19(33)16-13(30)6-12(29)7-14(16)37-22(23)10-2-4-11(28)5-3-10/h2-7,9,15,17-18,20-21,24-32,34-35H,8H2,1H3

> <INCHI_KEY>
NRVLSEXRPWZCQQ-UHFFFAOYSA-N

> <FORMULA>
C26H28O14

> <MOLECULAR_WEIGHT>
564.496

> <EXACT_MASS>
564.147905582

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.31949943248388

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)-4H-chromen-4-one

> <ALOGPS_LOGP>
0.48

> <JCHEM_LOGP>
0.06513928866666752

> <ALOGPS_LOGS>
-2.32

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.869700964057205

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.372347249855068

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981159828769554

> <JCHEM_POLAR_SURFACE_AREA>
225.05999999999997

> <JCHEM_REFRACTIVITY>
132.20170000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.68e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -4.359 -10.123   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.679  -8.617   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -3.535  -7.586   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -3.855  -6.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.711  -5.049   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.246  -5.525   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.770  -6.990   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.675  -8.236   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.770  -6.990   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.675  -8.236   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.207  -8.075   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.246  -5.525   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.320  -5.604   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -5.640  -4.098   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -6.464  -6.634   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -7.929  -6.158   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -6.144  -8.141   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -7.288  -9.171   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   39                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   35                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   13                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12    6   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   26                                                  
CONECT   16   15   17   28                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   25                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   18   26                                                  
CONECT   26   25   15   27                                                  
CONECT   27   26                                                            
CONECT   28   16   29   34                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   28                                                       
CONECT   35    4   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37    2   40                                                  
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₄

Average Mass

564.4960 Da

Monoisotopic Mass

564.14791 Da

IUPAC Name

5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one

CAS Registry Number

Not Available

SMILES

CC1OC(OC2C(OC3=C(OC4=CC(O)=CC(O)=C4C3=O)C3=CC=C(O)C=C3)OC(CO)C2O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C26H28O14/c1-9-17(31)20(34)21(35)25(36-9)40-24-18(32)15(8-27)38-26(24)39-23-19(33)16-13(30)6-12(29)7-14(16)37-22(23)10-2-4-11(28)5-3-10/h2-7,9,15,17-18,20-21,24-32,34-35H,8H2,1H3

InChI Key

NRVLSEXRPWZCQQ-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
Artabotrys hexapetalus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as depsides and depsidones. These are polycyclic compounds that is either a polyphenolic compound composed of two or more monocyclic aromatic units linked by an ester bond (depside), or a compound containing the depsidone structure (depsidone).

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Depsides and depsidones

Sub Class

Not Available

Direct Parent

Depsides and depsidones

Alternative Parents

Substituents

Depside backbone
Para-terphenyl
Terphenyl
Tetracarboxylic acid or derivatives
Biphenyl
Benzoate ester
Phenol ester
Benzoic acid or derivatives
Benzoyl
Phenoxy compound
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Carboxylic acid ester
Carboxylic acid derivative
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

phenols (CHEBI:65696 )
acetate ester (CHEBI:65696 )
benzoate ester (CHEBI:65696 )
para-terphenyl (CHEBI:65696 )

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	0.48	ALOGPS
logP	0.065	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	6.37	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	225.06 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	132.2 m³·mol⁻¹	ChemAxon
Polarizability	54.32 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73157235

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one (NP0258098)

MOL for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

3D MOL for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

3D SDF for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

3D-SDF for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

PDB for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

3D PDB for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

SMILES for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

INCHI for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

Structure for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)

3D Structure for NP0258098 (5,7-dihydroxy-3-{[4-hydroxy-5-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxolan-2-yl]oxy}-2-(4-hydroxyphenyl)chromen-4-one)