NP-MRD: Showing NP-Card for [(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid (NP0189746)

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Record Information

Version

2.0

Created at

2022-09-04 06:16:29 UTC

Updated at

2022-09-04 06:16:29 UTC

NP-MRD ID

NP0189746

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid

Description

2-[(2S,3S,4S)-5-(methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetic acid belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. [(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid is found in Calycophyllum spruceanum. Based on a literature review very few articles have been published on 2-[(2S,3S,4S)-5-(methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042208162D          

 35 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309042208162D          

 35 36  0  0  1  0            999 V2000
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 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 26 31  1  0  0  0  0
 10 31  1  0  0  0  0
 31 32  1  6  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0189746

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]([C@@H](C)OC(=O)C(\C)=C\C)[C@@H]1CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C22H32O13/c1-5-9(2)19(29)33-10(3)15-11(6-14(24)25)12(20(30)31-4)8-32-21(15)35-22-18(28)17(27)16(26)13(7-23)34-22/h5,8,10-11,13,15-18,21-23,26-28H,6-7H2,1-4H3,(H,24,25)/b9-5+/t10-,11-,13-,15-,16-,17+,18-,21+,22+/m1/s1

> <INCHI_KEY>
JVEXRQAKPOSWCW-WGOFRKARSA-N

> <FORMULA>
C22H32O13

> <MOLECULAR_WEIGHT>
504.485

> <EXACT_MASS>
504.18429109

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
49.30473367620472

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S,3S,4S)-5-(methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetic acid

> <JCHEM_LOGP>
-0.2180028323333327

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.207029977848702

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8568981309867154

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981084760188039

> <JCHEM_POLAR_SURFACE_AREA>
198.51

> <JCHEM_REFRACTIVITY>
114.61739999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3S,4S)-5-(methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   3.850   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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -9.336  -2.310   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  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       3.573  -4.326   0.000  0.00  0.00           O+0
HETATM   35  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    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   31                                                  
CONECT   11   10   12   24                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   13   23                                                  
CONECT   23   22                                                            
CONECT   24   11   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29                                                            
CONECT   31   26   10   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Value	Source
2-[(2S,3S,4S)-5-(Methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetate	Generator

Chemical Formula

C₂₂H₃₂O₁₃

Average Mass

504.4850 Da

Monoisotopic Mass

504.18429 Da

IUPAC Name

2-[(2S,3S,4S)-5-(methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetic acid

Traditional Name

[(2S,3S,4S)-5-(methoxycarbonyl)-3-[(1R)-1-{[(2E)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]acetic acid

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]([C@@H](C)OC(=O)C(\C)=C\C)[C@@H]1CC(O)=O

InChI Identifier

InChI=1S/C22H32O13/c1-5-9(2)19(29)33-10(3)15-11(6-14(24)25)12(20(30)31-4)8-32-21(15)35-22-18(28)17(27)16(26)13(7-23)34-22/h5,8,10-11,13,15-18,21-23,26-28H,6-7H2,1-4H3,(H,24,25)/b9-5+/t10-,11-,13-,15-,16-,17+,18-,21+,22+/m1/s1

InChI Key

JVEXRQAKPOSWCW-WGOFRKARSA-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
Calycophyllum spruceanum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Glycosyl compound
Secoiridoid-skeleton
O-glycosyl compound
Monocyclic monoterpenoid
Monoterpenoid
Tricarboxylic acid or derivatives
Fatty acid ester
Monosaccharide
Fatty acyl
Oxane
Vinylogous ester
Enoate ester
Methyl ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Polyol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Acetal
Organoheterocyclic compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Primary alcohol
Alcohol
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-0.22	ChemAxon
pKa (Strongest Acidic)	3.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	198.51 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	114.62 m³·mol⁻¹	ChemAxon
Polarizability	49.3 Å³	ChemAxon
Number of Rings	2	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

32055216

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162904991

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid (NP0189746)

MOL for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

3D MOL for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

3D SDF for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

3D-SDF for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

PDB for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

3D PDB for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

SMILES for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

INCHI for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

Structure for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)

3D Structure for NP0189746 ([(2s,3s,4s)-5-(methoxycarbonyl)-3-[(1r)-1-{[(2e)-2-methylbut-2-enoyl]oxy}ethyl]-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]acetic acid)