NP-MRD: Showing NP-Card for 8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one (NP0252182)

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Record Information

Version

2.0

Created at

2022-09-07 15:36:49 UTC

Updated at

2022-09-07 15:36:49 UTC

NP-MRD ID

NP0252182

Secondary Accession Numbers

None

Natural Product Identification

Common Name

8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

Description

NP-000004(11) belongs to the class of organic compounds known as flavonoid 8-c-glycosides. Flavonoid 8-C-glycosides are compounds containing a carbohydrate moiety which is C-glycosidically linked to 8-position of a 2-phenylchromen-4-one flavonoid backbone. 8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one is found in Gnetum africanum. NP-000004(11) is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004191513372D          

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M  END

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  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  0  0  0  0
 13 25  2  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 10 33  1  0  0  0  0
 27 33  2  0  0  0  0
 31 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 37 39  1  0  0  0  0
 39 40  2  0  0  0  0
 34 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0252182

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(C(O)C1O)C1=C(O)C(C2OC(CO)C(O)C(O)C2O)=C(O)C2=C1OC(=CC2=O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O14/c27-6-12-17(31)21(35)23(37)25(39-12)15-19(33)14-10(30)5-11(8-1-3-9(29)4-2-8)38-24(14)16(20(15)34)26-22(36)18(32)13(7-28)40-26/h1-5,12-13,17-18,21-23,25-29,31-37H,6-7H2

> <INCHI_KEY>
TUIJPUWSXVFWSH-UHFFFAOYSA-N

> <FORMULA>
C26H28O14

> <MOLECULAR_WEIGHT>
564.496

> <EXACT_MASS>
564.147905582

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.54190844892853

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one

> <ALOGPS_LOGP>
-0.70

> <JCHEM_LOGP>
-2.1776177343333334

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.6301494242860315

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.737497458898625

> <JCHEM_PKA_STRONGEST_BASIC>
-3.644730893437341

> <JCHEM_POLAR_SURFACE_AREA>
247.05999999999995

> <JCHEM_REFRACTIVITY>
133.18799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.39e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       1.619  -9.643   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.992  -8.236   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.897  -6.990   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.421  -5.525   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.913  -5.525   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.378  -5.049   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.437  -6.990   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.343  -8.236   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    3    9                                                  
CONECT    9    8                                                            
CONECT   10    5   11   33                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   25                                                  
CONECT   14   13   15   23                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   14   24                                                  
CONECT   24   23                                                            
CONECT   25   13   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   33                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32   34                                                  
CONECT   32   31   33                                                       
CONECT   33   32   10   27                                                  
CONECT   34   31   35   40                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39   34                                                       
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

8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one

Traditional Name

8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

CAS Registry Number

Not Available

SMILES

OCC1OC(C(O)C1O)C1=C(O)C(C2OC(CO)C(O)C(O)C2O)=C(O)C2=C1OC(=CC2=O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C26H28O14/c27-6-12-17(31)21(35)23(37)25(39-12)15-19(33)14-10(30)5-11(8-1-3-9(29)4-2-8)38-24(14)16(20(15)34)26-22(36)18(32)13(7-28)40-26/h1-5,12-13,17-18,21-23,25-29,31-37H,6-7H2

InChI Key

TUIJPUWSXVFWSH-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
Gnetum africanum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid 8-c-glycosides. Flavonoid 8-C-glycosides are compounds containing a carbohydrate moiety which is C-glycosidically linked to 8-position of a 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid 8-C-glycosides

Alternative Parents

Substituents

Flavonoid-8-c-glycoside
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavone
Hydroxyflavonoid
Phenolic glycoside
C-glycosyl compound
Chromone
Glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Pyran
Oxolane
Heteroaromatic compound
Vinylogous acid
1,2-diol
Secondary alcohol
Polyol
Oxacycle
Organoheterocyclic compound
Dialkyl ether
Ether
Organic oxide
Organic oxygen compound
Primary alcohol
Alcohol
Organooxygen compound
Hydrocarbon derivative
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	-0.7	ALOGPS
logP	-2.2	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	5.74	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	247.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	133.19 m³·mol⁻¹	ChemAxon
Polarizability	54.54 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	No	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

10053626

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one (NP0252182)

MOL for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

3D MOL for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

3D SDF for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

3D-SDF for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

PDB for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

3D PDB for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

SMILES for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

INCHI for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

Structure for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)

3D Structure for NP0252182 (8-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one)