NP-MRD: Showing NP-Card for 2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0309346)

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Record Information

Version

2.0

Created at

2022-09-11 03:53:12 UTC

Updated at

2022-09-11 03:53:12 UTC

NP-MRD ID

NP0309346

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Description

(2R)-1-O-beta-D-Galactopyranosylglycerol, also known as (2R)-glyceryl-beta-D-galactopyranoside or alpha-galactosylglycerol, belongs to the class of organic compounds known as glycosylglycerols. These are glycerolipids structurally characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage (2R)-1-O-beta-D-Galactopyranosylglycerol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (2R)-1-O-beta-D-Galactopyranosylglycerol has been detected, but not quantified in, cereals and cereal products. 2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol is found in Acca sellowiana, Lilium japonicum, Lilium lancifolium and Carteriospongia foliascens. This could make (2R)-1-O-beta-D-galactopyranosylglycerol a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
   -1.8944    2.0321    2.4456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5136    1.3135    1.3996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8294   -0.0488    1.3803 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4856    0.0579    1.1521 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1056    0.4716   -0.0950 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2019    0.0390   -0.2912 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0276    1.1175   -0.4791 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4506    0.5847   -0.6897 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4941   -0.2476   -1.8057 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7951   -0.1986    0.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8412   -1.2222    0.6662 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9354   -0.0753   -1.2194 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1238   -0.4826   -2.2774 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7874   -1.2483   -0.8223 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9690   -2.3759   -0.7679 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5379   -1.0136    0.4625 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8090   -0.5505    0.1357 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7465    2.9718    2.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5727    1.1788    1.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3887    1.8223    0.4340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9507   -0.4524    2.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1011    1.5703   -0.1478 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9802    1.8119    0.3568 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6940    1.6698   -1.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1455    1.4365   -0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7266   -0.0825   -2.4018 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6937    0.5072    1.4099 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7938   -0.6441    0.4809 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1940   -2.0215    1.1137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5813    0.7512   -1.6382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4565   -1.2953   -2.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5042   -1.4227   -1.6598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7327   -2.5788    0.1599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6728   -2.0123    0.9510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3400   -1.3632   -0.1438 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  8  1  0
  8  9  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
  3 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  1  0
 14 12  1  0
 12 13  1  0
 12  5  1  0
 11 29  1  0
 10 27  1  0
 10 28  1  0
  8 25  1  6
  9 26  1  0
  7 23  1  0
  7 24  1  0
  5 22  1  1
  3 21  1  1
  2 19  1  0
  2 20  1  0
  1 18  1  0
 16 34  1  1
 17 35  1  0
 14 32  1  6
 15 33  1  0
 12 30  1  6
 13 31  1  0
M  END

Structure #1
  Mrv0541 02241206352D          

 17 17  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1 10  1  0  0  0  0
  2  5  1  0  0  0  0
  2 11  1  0  0  0  0
  3  4  1  0  0  0  0
  3 16  1  0  0  0  0
  4 12  1  0  0  0  0
  5  6  1  0  0  0  0
  5 17  1  0  0  0  0
  6  7  1  0  0  0  0
  6 13  1  0  0  0  0
  7  8  1  0  0  0  0
  7 14  1  0  0  0  0
  8  9  1  0  0  0  0
  8 15  1  0  0  0  0
  9 16  1  0  0  0  0
  9 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0309346

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(O)COC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H18O8/c10-1-4(12)3-16-9-8(15)7(14)6(13)5(2-11)17-9/h4-15H,1-3H2

> <INCHI_KEY>
NHJUPBDCSOGIKX-UHFFFAOYSA-N

> <FORMULA>
C9H18O8

> <MOLECULAR_WEIGHT>
254.2344

> <EXACT_MASS>
254.100167552

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
24.256402180256487

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-2.80

> <JCHEM_LOGP>
-3.6098496683333328

> <ALOGPS_LOGS>
0.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.08057270985643

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.194840023983808

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9682677554533683

> <JCHEM_POLAR_SURFACE_AREA>
139.84

> <JCHEM_REFRACTIVITY>
52.9294

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.60e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      13.337   6.160   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      13.337   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      10.669   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       8.002   4.620   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
CONECT    1    4   10                                                       
CONECT    2    5   11                                                       
CONECT    3    4   16                                                       
CONECT    4    1    3   12                                                  
CONECT    5    2    6   17                                                  
CONECT    6    5    7   13                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9   15                                                  
CONECT    9    8   16   17                                                  
CONECT   10    1                                                            
CONECT   11    2                                                            
CONECT   12    4                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
CONECT   16    3    9                                                       
CONECT   17    5    9                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
(2R)-1-O-b-D-Galactopyranosylglycerol	Generator
(2R)-1-O-Β-D-galactopyranosylglycerol	Generator
(2R)-Glyceryl-beta-D-galactopyranoside	HMDB
(beta-D)-Isomer OF isofloridoside	HMDB
D-Glyceryl beta-galactopyranoside	HMDB
alpha-Galactosylglycerol	HMDB
(beta-D)-(S)-Isomer OF isofloridoside	HMDB
3-O-Galactopyranosyl-sn-glycerol	HMDB
(beta-D)-(R)-Isomer OF isofloridoside	HMDB
Galactoside, 2,3-dihydroxypropyl OF isofloridoside	HMDB
(R)-Isomer OF isofloridoside	HMDB
beta-D-Galactoside, 2,3-dihydroxypropyl OF isofloridoside	HMDB
3-O-Galactopyranosylglycerol	HMDB
Isofloridoside	HMDB

Chemical Formula

C₉H₁₈O₈

Average Mass

254.2344 Da

Monoisotopic Mass

254.10017 Da

IUPAC Name

2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OCC(O)COC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C9H18O8/c10-1-4(12)3-16-9-8(15)7(14)6(13)5(2-11)17-9/h4-15H,1-3H2

InChI Key

NHJUPBDCSOGIKX-UHFFFAOYSA-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
Acca sellowiana	LOTUS Database	35616633
Lilium japonicum	LOTUS Database	35616633
Lilium tigrinum	LOTUS Database	35616633
Phyllospongia foliascens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylglycerols. These are glycerolipids structurally characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerolipids

Sub Class

Glycosylglycerols

Direct Parent

Glycosylglycerols

Alternative Parents

Substituents

Glycosylglycerol
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Secondary alcohol
Polyol
Oxacycle
Acetal
Organoheterocyclic compound
Primary alcohol
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

a small molecule (3-B-D-GALACTOSYL-SN-GLYCEROL )

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	-2.8	ALOGPS
logP	-3.6	ChemAxon
logS	0.15	ALOGPS
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	139.84 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	52.93 m³·mol⁻¹	ChemAxon
Polarizability	24.26 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0038664

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB018063

KNApSAcK ID

Not Available

Chemspider ID

3507968

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

4302177

PDB ID

Not Available

ChEBI ID

144569

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0309346)

MOL for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0309346 (2-(2,3-dihydroxypropoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)