NP-MRD: Showing NP-Card for 2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol (NP0287876)

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Record Information

Version

2.0

Created at

2022-09-09 17:20:58 UTC

Updated at

2022-09-09 17:20:58 UTC

NP-MRD ID

NP0287876

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Description

Raffinose 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. Raffinose is an extremely weak basic (essentially neutral) compound (based on its pKa). Within humans, raffinose participates in a number of enzymatic reactions. In particular, raffinose and D-galactose can be biosynthesized from stachyose; which is mediated by the enzyme Alpha-galactosidase a. In addition, raffinose can be converted into sucrose and D-galactose through the action of the enzyme Alpha-galactosidase a. The enzyme does not cleave β-linked galactose, as in lactose. In humans, raffinose is involved in galactose metabolism. Outside of the human body, Raffinose is found, on average, in the highest concentration within a few different foods, such as ginkgo nuts, soy beans, and mung beans and in a lower concentration in gram beans, dates, and coconuts. Raffinose has also been detected, but not quantified in, several different foods, such as summer savories, mexican groundcherries, summer grapes, american cranberries, and common hazelnuts. This could make raffinose a potential biomarker for the consumption of these foods. Either raffinose or sucrose is used as a base substance for sucralose. Raffinose is a trisaccharide composed of galactose, glucose, and fructose. These oligosaccharides pass undigested through the stomach and upper intestine. The raffinose family of oligosaccharides (RFOs) are alpha-galactosyl derivatives of sucrose, and the most common are the trisaccharide raffinose, the tetrasaccharide stachyose, and the pentasaccharide verbascose. In the lower intestine, they are fermented by gas-producing bacteria that do possess the α-GAL enzyme and make short-chain fatty acids (SCFA)(acetic, propionic, butyric acids) commonly associated with eating beans and other vegetables. 2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol is found in Arabidopsis thaliana, Origanum vulgare, Rehmannia glutinosa and Salacia oblonga. Raffinose can be hydrolyzed to D-galactose and sucrose by the enzyme α-galactosidase (α-GAL), an enzyme not found in the human digestive tract.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305221920192D          

 34 36  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652305221920192D          

 34 36  0  0  0  0            999 V2000
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 32 17  1  0  0  0  0
 33  6  1  0  0  0  0
 33 18  1  0  0  0  0
 34 17  1  0  0  0  0
 34 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0287876

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(CO)(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(O)C2O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C18H32O16/c19-1-5-8(22)11(25)13(27)16(31-5)30-3-7-9(23)12(26)14(28)17(32-7)34-18(4-21)15(29)10(24)6(2-20)33-18/h5-17,19-29H,1-4H2

> <INCHI_KEY>
MUPFEKGTMRGPLJ-UHFFFAOYSA-N

> <FORMULA>
C18H32O16

> <MOLECULAR_WEIGHT>
504.4371

> <EXACT_MASS>
504.169034976

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
47.00269549334201

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-3.36

> <JCHEM_LOGP>
-6.299670609333333

> <ALOGPS_LOGS>
0.12

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.148641922410812

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.695274801560533

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483773177512537

> <JCHEM_POLAR_SURFACE_AREA>
268.67999999999995

> <JCHEM_REFRACTIVITY>
101.1874

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.69e+02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       9.810  16.652   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.397   3.560   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.212  13.538   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.042   8.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.303  16.972   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.302   4.806   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.181  12.394   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.827  18.436   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.675  12.714   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.842   4.806   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.321  18.757   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.645  11.570   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.290  17.612   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.120  10.105   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.318   6.271   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.766  16.148   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.627   9.785   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.072   7.176   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.840  17.796   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       2.023   2.153   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.535   8.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       8.858  19.581   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       2.199  14.179   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.747   3.560   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.845  20.221   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.138  11.890   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       3.784  17.932   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.090   8.961   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       5.783   6.747   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.736  15.003   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       7.273  15.827   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       4.657  10.929   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       1.826   6.271   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       4.103   8.320   0.000  0.00  0.00           O+0
CONECT    1    5   19                                                       
CONECT    2    6   20                                                       
CONECT    3    7   30                                                       
CONECT    4   18   21                                                       
CONECT    5    1    8   31                                                  
CONECT    6    2   10   33                                                  
CONECT    7    3    9   32                                                  
CONECT    8    5   11   22                                                  
CONECT    9    7   12   23                                                  
CONECT   10    6   15   24                                                  
CONECT   11    8   13   25                                                  
CONECT   12    9   14   26                                                  
CONECT   13   11   16   27                                                  
CONECT   14   12   17   28                                                  
CONECT   15   10   18   29                                                  
CONECT   16   13   30   31                                                  
CONECT   17   14   32   34                                                  
CONECT   18    4   15   33   34                                             
CONECT   19    1                                                            
CONECT   20    2                                                            
CONECT   21    4                                                            
CONECT   22    8                                                            
CONECT   23    9                                                            
CONECT   24   10                                                            
CONECT   25   11                                                            
CONECT   26   12                                                            
CONECT   27   13                                                            
CONECT   28   14                                                            
CONECT   29   15                                                            
CONECT   30    3   16                                                       
CONECT   31    5   16                                                       
CONECT   32    7   17                                                       
CONECT   33    6   18                                                       
CONECT   34   17   18                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
b-D-Fructofuranosyl O-b-D-glucopyranosyl-(1->6)-a-D-glucopyranoside, 9ci, 8ci	HMDB
b-D-Glucopyranosyl-(1->6)-a-D-glucopyranosyl-(1->2)-b-D-fructofuranoside	HMDB
beta-D-GLCP-(1->6)-alpha-D-GLCP-(12)-beta-D-fruf	HMDB

Chemical Formula

C₁₈H₃₂O₁₆

Average Mass

504.4371 Da

Monoisotopic Mass

504.16903 Da

IUPAC Name

2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OCC1OC(CO)(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(O)C2O)C(O)C1O

InChI Identifier

InChI=1S/C18H32O16/c19-1-5-8(22)11(25)13(27)16(31-5)30-3-7-9(23)12(26)14(28)17(32-7)34-18(4-21)15(29)10(24)6(2-20)33-18/h5-17,19-29H,1-4H2

InChI Key

MUPFEKGTMRGPLJ-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
Arabidopsis thaliana	LOTUS Database	35616633
Origanum vulgare	LOTUS Database	35616633
Rehmannia glutinosa	LOTUS Database	35616633
Salacia oblonga	LOTUS Database	35616633

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
C-glycosyl compound
Glycosyl compound
O-glycosyl compound
Ketal
Oxane
Tetrahydrofuran
Secondary alcohol
Acetal
Oxacycle
Organoheterocyclic compound
Polyol
Alcohol
Primary alcohol
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

a trisaccharide (CPD-1099 )

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	-3.4	ALOGPS
logP	-6.3	ChemAxon
logS	0.12	ALOGPS
pKa (Strongest Acidic)	11.7	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	268.68 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	101.19 m³·mol⁻¹	ChemAxon
Polarizability	47 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

FDB000661

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Raffinose

METLIN ID

Not Available

PubChem Compound

219993

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol (NP0287876)

MOL for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0287876 (2-[(6-{[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl)methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)