NP-MRD: Showing NP-Card for 6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one (NP0303124)

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Record Information

Version

2.0

Created at

2022-09-10 17:12:20 UTC

Updated at

2022-09-10 17:12:20 UTC

NP-MRD ID

NP0303124

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

6-[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one 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. 6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one is found in Trigastrotheca pentaphylla. Based on a literature review very few articles have been published on 6-[(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102219122D          

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M  END

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  Mrv1652309102219122D          

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 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  1  0  0  0
 14 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 27 26  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
 27 34  1  0  0  0  0
 34 35  1  1  0  0  0
 26 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  2  0  0  0  0
  2 38  1  0  0  0  0
 13 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0303124

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@H]1O)C1=C(O)C([C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H26O13/c26-6-12-17(30)21(34)24(37-12)15-19(32)14-10(29)5-11(8-1-3-9(28)4-2-8)36-23(14)16(20(15)33)25-22(35)18(31)13(7-27)38-25/h1-5,12-13,17-18,21-22,24-28,30-35H,6-7H2/t12-,13+,17+,18+,21-,22-,24+,25+/m1/s1

> <INCHI_KEY>
CYCBZRWDLPMQPC-ONKNSGEJSA-N

> <FORMULA>
C25H26O13

> <MOLECULAR_WEIGHT>
534.47

> <EXACT_MASS>
534.137340897

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
51.26604473594066

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-1.5472827923333337

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.63015096252583

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.737497482625178

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9791998238445334

> <JCHEM_POLAR_SURFACE_AREA>
226.82999999999996

> <JCHEM_REFRACTIVITY>
127.2255

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.089   2.445   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.565   3.910   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.660   5.156   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.286   6.563   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.105   3.910   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.010   5.156   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.581   2.445   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       8.045   1.969   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.409  -2.454   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.439  -3.598   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.971  -3.437   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      12.597  -2.030   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.669  -4.932   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.296  -6.339   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       8.163  -4.612   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.019  -5.642   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   38                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    5                                                       
CONECT   12    4   13                                                       
CONECT   13   12   14   38                                                  
CONECT   14   13   15   24                                                  
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   15   23                                                  
CONECT   23   22                                                            
CONECT   24   14   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   36                                                  
CONECT   27   26   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   27   35                                                  
CONECT   35   34                                                            
CONECT   36   26   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36    2   13                                                  
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₆O₁₃

Average Mass

534.4700 Da

Monoisotopic Mass

534.13734 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@H]1O)C1=C(O)C([C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C25H26O13/c26-6-12-17(30)21(34)24(37-12)15-19(32)14-10(29)5-11(8-1-3-9(28)4-2-8)36-23(14)16(20(15)33)25-22(35)18(31)13(7-27)38-25/h1-5,12-13,17-18,21-22,24-28,30-35H,6-7H2/t12-,13+,17+,18+,21-,22-,24+,25+/m1/s1

InChI Key

CYCBZRWDLPMQPC-ONKNSGEJSA-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
Mollugo pentaphylla	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
Hydroxyflavonoid
Flavone
Phenolic glycoside
C-glycosyl compound
Chromone
Glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Pyran
Benzenoid
Monocyclic benzene moiety
Monosaccharide
Heteroaromatic compound
Vinylogous acid
Tetrahydrofuran
Secondary alcohol
Ether
Dialkyl ether
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Organooxygen compound
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	-1.5	ChemAxon
pKa (Strongest Acidic)	5.74	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	226.83 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	127.23 m³·mol⁻¹	ChemAxon
Polarizability	51.27 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

162991024

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one (NP0303124)

MOL for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

3D MOL for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

3D SDF for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

3D-SDF for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

PDB for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

3D PDB for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

SMILES for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

INCHI for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

Structure for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)

3D Structure for NP0303124 (6-[(2s,3r,4r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-8-[(2s,3r,4r,5s)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one)