NP-MRD: Showing NP-Card for (2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid (NP0257765)

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Record Information

Version

2.0

Created at

2022-09-07 22:58:53 UTC

Updated at

2022-09-07 22:58:53 UTC

NP-MRD ID

NP0257765

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Description

(2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds. Based on a literature review very few articles have been published on (2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082200582D          

 35 37  0  0  1  0            999 V2000
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309082200582D          

 35 37  0  0  1  0            999 V2000
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0257765

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H30O17/c19-1-3-5(21)8(24)14(35-17-10(26)7(23)9(25)13(34-17)15(28)29)18(32-3)33-12-6(22)4(2-20)31-16(30)11(12)27/h3-14,16-27,30H,1-2H2,(H,28,29)/t3-,4-,5-,6-,7+,8+,9+,10-,11-,12+,13+,14+,16+,17+,18+/m1/s1

> <INCHI_KEY>
MORJZMNZWXVGAZ-JMJYNTRKSA-N

> <FORMULA>
C18H30O17

> <MOLECULAR_WEIGHT>
518.421

> <EXACT_MASS>
518.148299506

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
46.1237704270582

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <JCHEM_LOGP>
-6.153935971333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.254742594374871

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1344324420250236

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6855122702867957

> <JCHEM_POLAR_SURFACE_AREA>
285.75

> <JCHEM_REFRACTIVITY>
100.61740000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.003 -11.550   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.669 -13.860   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       9.336 -14.630   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.669 -16.940   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.668 -14.630   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   34                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   30                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   28                                                  
CONECT    9    8   10   22                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   20                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   11   21                                                  
CONECT   21   20                                                            
CONECT   22    9   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26    8   29                                                  
CONECT   29   28                                                            
CONECT   30    6   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    4   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Value	Source
(2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylate	Generator

Chemical Formula

C₁₈H₃₀O₁₇

Average Mass

518.4210 Da

Monoisotopic Mass

518.14830 Da

IUPAC Name

(2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

(2S,3S,4S,5R,6R)-6-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2S,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)O[C@H](CO)[C@H]2O)[C@@H](O[C@@H]2O[C@@H]([C@@H](O)[C@H](O)[C@H]2O)C(O)=O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C18H30O17/c19-1-3-5(21)8(24)14(35-17-10(26)7(23)9(25)13(34-17)15(28)29)18(32-3)33-12-6(22)4(2-20)31-16(30)11(12)27/h3-14,16-27,30H,1-2H2,(H,28,29)/t3-,4-,5-,6-,7+,8+,9+,10-,11-,12+,13+,14+,16+,17+,18+/m1/s1

InChI Key

MORJZMNZWXVGAZ-JMJYNTRKSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

Alternative Parents

Substituents

Oligosaccharide
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Glycosyl compound
O-glycosyl compound
Beta-hydroxy acid
Pyran
Hydroxy acid
Oxane
Hemiacetal
Secondary alcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Primary alcohol
Alcohol
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	-6.2	ChemAxon
pKa (Strongest Acidic)	3.13	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	285.75 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	100.62 m³·mol⁻¹	ChemAxon
Polarizability	46.12 Å³	ChemAxon
Number of Rings	3	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

163021420

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,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid (NP0257765)

MOL for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

3D MOL for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

3D SDF for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

3D-SDF for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

PDB for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

3D PDB for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

SMILES for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

INCHI for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

Structure for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)

3D Structure for NP0257765 ((2s,3s,4s,5r,6r)-6-{[(2s,3s,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(2s,3r,4s,5r,6r)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}oxan-3-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid)