NP-MRD: Showing NP-Card for (2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol (NP0209005)

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Record Information

Version

2.0

Created at

2022-09-05 06:14:24 UTC

Updated at

2022-09-05 06:14:24 UTC

NP-MRD ID

NP0209005

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol

Description

Benzyl 2-O-(D-apio-beta-D-furanosyl)-6-O-(beta-D-xylopyranosyl)-beta-D-glucopyranoside belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Based on a literature review very few articles have been published on Benzyl 2-O-(D-apio-beta-D-furanosyl)-6-O-(beta-D-xylopyranosyl)-beta-D-glucopyranoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052208142D          

 37 40  0  0  1  0            999 V2000
    2.5608    1.1513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3059    0.3667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1904   -0.7313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -1.5160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.7553   -2.1834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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  Mrv1652309052208142D          

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 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  1  0  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 17 24  1  0  0  0  0
 24 25  1  1  0  0  0
 14 26  1  0  0  0  0
 26 27  1  0  0  0  0
  9 27  1  0  0  0  0
 27 28  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 30 35  1  0  0  0  0
  7 36  1  0  0  0  0
  3 36  1  0  0  0  0
 36 37  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0209005

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@]1(O)CO[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O[C@H]2OCC2=CC=CC=C2)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H34O14/c24-9-23(31)10-35-22(19(23)30)37-18-16(28)15(27)13(8-34-20-17(29)14(26)12(25)7-33-20)36-21(18)32-6-11-4-2-1-3-5-11/h1-5,12-22,24-31H,6-10H2/t12-,13-,14+,15-,16+,17-,18-,19+,20+,21-,22+,23-/m1/s1

> <INCHI_KEY>
YWHJEIFJXPWKSU-UMJNWNEHSA-N

> <FORMULA>
C23H34O14

> <MOLECULAR_WEIGHT>
534.511

> <EXACT_MASS>
534.194855775

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
52.72044185278318

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R)-2-{[(2R,3S,4S,5R,6R)-6-(benzyloxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol

> <JCHEM_LOGP>
-2.981939360666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.23095707548744

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.67332971125156

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423791405601023

> <JCHEM_POLAR_SURFACE_AREA>
217.21999999999997

> <JCHEM_REFRACTIVITY>
118.40820000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5R)-2-{[(2R,3S,4S,5R,6R)-6-(benzyloxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0       4.780   2.149   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.304   0.684   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335  -0.460   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.365   0.684   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.089  -1.365   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.565  -2.830   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.105  -2.830   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.010  -4.076   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.384  -5.483   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.289  -6.728   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.820  -6.567   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.662  -8.135   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       7.568  -9.381   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.131  -8.296   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.504  -9.703   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.410 -10.949   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.783 -12.356   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.688 -13.602   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.062 -15.009   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.530 -15.170   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.904 -16.576   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.625 -13.924   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.094 -14.085   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       3.252 -12.517   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.346 -11.271   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.226  -7.050   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.852  -5.644   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       3.947  -4.398   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.415  -4.559   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.510  -3.313   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.022  -3.474   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.927  -2.228   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.300  -0.821   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.231  -0.660   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.136  -1.906   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.581  -1.365   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       8.045  -0.889   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5   36                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   36                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   27                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   26                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   17   25                                                  
CONECT   25   24                                                            
CONECT   26   14   27                                                       
CONECT   27   26    9   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   35                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   30                                                       
CONECT   36    7    3   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Value	Source
Benzyl 2-O-(D-apio-b-D-furanosyl)-6-O-(b-D-xylopyranosyl)-b-D-glucopyranoside	Generator
Benzyl 2-O-(D-apio-β-D-furanosyl)-6-O-(β-D-xylopyranosyl)-β-D-glucopyranoside	Generator

Chemical Formula

C₂₃H₃₄O₁₄

Average Mass

534.5110 Da

Monoisotopic Mass

534.19486 Da

IUPAC Name

(2S,3R,4S,5R)-2-{[(2R,3S,4S,5R,6R)-6-(benzyloxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5R)-2-{[(2R,3S,4S,5R,6R)-6-(benzyloxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OC[C@@]1(O)CO[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O[C@H]2OCC2=CC=CC=C2)[C@@H]1O

InChI Identifier

InChI=1S/C23H34O14/c24-9-23(31)10-35-22(19(23)30)37-18-16(28)15(27)13(8-34-20-17(29)14(26)12(25)7-33-20)36-21(18)32-6-11-4-2-1-3-5-11/h1-5,12-22,24-31H,6-10H2/t12-,13-,14+,15-,16+,17-,18-,19+,20+,21-,22+,23-/m1/s1

InChI Key

YWHJEIFJXPWKSU-UMJNWNEHSA-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 o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Disaccharide
O-glycosyl compound
Monocyclic benzene moiety
Oxane
Benzenoid
Oxolane
Tertiary alcohol
Secondary alcohol
Polyol
Oxacycle
Acetal
Organoheterocyclic compound
Primary alcohol
Alcohol
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-3	ChemAxon
pKa (Strongest Acidic)	11.67	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	217.22 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	118.41 m³·mol⁻¹	ChemAxon
Polarizability	52.72 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

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

102066455

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol (NP0209005)

MOL for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

3D MOL for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

3D SDF for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

3D-SDF for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

PDB for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

3D PDB for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

SMILES for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

INCHI for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

Structure for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)

3D Structure for NP0209005 ((2s,3r,4s,5r)-2-{[(2r,3s,4s,5r,6r)-6-(benzyloxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]methoxy}oxane-3,4,5-triol)