NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0296579)

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Record Information

Version

2.0

Created at

2022-09-10 06:14:29 UTC

Updated at

2022-09-10 06:14:29 UTC

NP-MRD ID

NP0296579

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

Glochiflavanoside B belongs to the class of organic compounds known as flavonoid-7-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C7-position. (2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Glochidion zeylanicum. (2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol was first documented in 2011 (PMID: 22115036). Based on a literature review very few articles have been published on Glochiflavanoside B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102208142D          

 36 39  0  0  1  0            999 V2000
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   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    0.8250    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
    0.7145   -0.4125    0.0000 C   0  0  1  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
    2.1434   -0.4125    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
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309102208142D          

 36 39  0  0  1  0            999 V2000
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  6 29  1  0  0  0  0
 29 30  1  6  0  0  0
  5 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 32 35  2  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0296579

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O)[C@H]1OC2=CC(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)=CC(OC)=C2C[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H30O12/c1-31-14-6-11(34-24-22(30)21(29)20(28)18(9-25)36-24)7-15-12(14)8-13(26)23(35-15)10-4-16(32-2)19(27)17(5-10)33-3/h4-7,13,18,20-30H,8-9H2,1-3H3/t13-,18+,20+,21-,22+,23+,24+/m0/s1

> <INCHI_KEY>
CWNQCRVGOLTLSA-MTGIANMYSA-N

> <FORMULA>
C24H30O12

> <MOLECULAR_WEIGHT>
510.492

> <EXACT_MASS>
510.173726406

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
51.14907731724895

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2R,3S)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-0.3388442316666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.191943483277464

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.299722981875133

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923437586494

> <JCHEM_POLAR_SURFACE_AREA>
176.76

> <JCHEM_REFRACTIVITY>
121.57189999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(2R,3S)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <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  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   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  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      10.669  -0.000   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      13.337   1.540   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   31                                                  
CONECT    6    5    7   29                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   27                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   23                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   12   22                                                  
CONECT   22   21                                                            
CONECT   23   10   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24    8   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28    6   30                                                  
CONECT   30   29                                                            
CONECT   31    5   32                                                       
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32    3   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₀O₁₂

Average Mass

510.4920 Da

Monoisotopic Mass

510.17373 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(2R,3S)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5S,6R)-2-{[(2R,3S)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O)[C@H]1OC2=CC(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)=CC(OC)=C2C[C@@H]1O

InChI Identifier

InChI=1S/C24H30O12/c1-31-14-6-11(34-24-22(30)21(29)20(28)18(9-25)36-24)7-15-12(14)8-13(26)23(35-15)10-4-16(32-2)19(27)17(5-10)33-3/h4-7,13,18,20-30H,8-9H2,1-3H3/t13-,18+,20+,21-,22+,23+,24+/m0/s1

InChI Key

CWNQCRVGOLTLSA-MTGIANMYSA-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
Glochidion zeylanicum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-7-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C7-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-7-O-glycosides

Alternative Parents

Substituents

Flavonoid-7-o-glycoside
Epigallocatechin
Catechin
3p-methoxyflavonoid-skeleton
5-methoxyflavonoid-skeleton
3-hydroxyflavonoid
Hydroxyflavonoid
4'-hydroxyflavonoid
Flavan-3-ol
Flavan
Fatty acyl glycoside
Phenolic glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Chromane
Benzopyran
M-dimethoxybenzene
Dimethoxybenzene
1-benzopyran
Methoxyphenol
Phenol ether
Methoxybenzene
Anisole
Phenoxy compound
Phenol
Alkyl aryl ether
Oxane
Monosaccharide
Benzenoid
Monocyclic benzene moiety
Fatty acyl
Secondary alcohol
Organoheterocyclic compound
Acetal
Oxacycle
Ether
Polyol
Primary alcohol
Organooxygen compound
Alcohol
Organic oxygen 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	-0.34	ChemAxon
pKa (Strongest Acidic)	9.3	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	176.76 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	121.57 m³·mol⁻¹	ChemAxon
Polarizability	51.15 Å³	ChemAxon
Number of Rings	4	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

9278360

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11103219

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Saleem M, Akhtar N, Riaz N, Ali MS, Jabbar A: Isolation and characterization of secondary metabolites from Plumeria obtusa. J Asian Nat Prod Res. 2011 Dec;13(12):1122-7. doi: 10.1080/10286020.2011.618452. [PubMed:22115036 ]
LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0296579)

MOL for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0296579 ((2s,3r,4s,5s,6r)-2-{[(2r,3s)-3-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2h-1-benzopyran-7-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)