NP-MRD: Showing NP-Card for (2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 (NP0183744)

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Record Information

Version

2.0

Created at

2022-09-03 22:42:17 UTC

Updated at

2022-09-03 22:42:17 UTC

NP-MRD ID

NP0183744

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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

Gentianose 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. Gentianose is an extremely weak basic (essentially neutral) compound (based on its pKa). (2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 Gentiana algida, Gentiana linearis and Gentiana lutea. (2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 was first documented in 1951 (PMID: 14935697). A trisaccharide composed of beta-D-glucopyranose, alpha-D-glucopyranose and beta-D-fructofuranose units (PMID: 24257774) (PMID: 8588862).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305251900022D          

 34 36  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652305251900022D          

 34 36  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0183744

> <DATABASE_NAME>
NP-MRD

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

> <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/t5-,6-,7-,8-,9-,10-,11+,12+,13-,14-,15+,16-,17-,18+/m1/s1

> <INCHI_KEY>
MUPFEKGTMRGPLJ-WSCXOGSTSA-N

> <FORMULA>
C18H32O16

> <MOLECULAR_WEIGHT>
504.438

> <EXACT_MASS>
504.16903495

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
46.76594831732119

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)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>
101.18739999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.69e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gentianose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-19         0                                  
HETATM    1  O   UNK     0    8665.8798671.690   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8664.9318668.221   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8661.5878668.233   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8660.7168671.690   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8659.3838670.920   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8668.5438667.070   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    8669.8768666.301   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8672.5448661.680   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8673.8768662.449   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8667.2078664.761   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8667.2078661.680   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8669.8768660.140   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8668.5438673.230   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8671.2168671.690   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0    8671.2168668.610   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0    8664.6498672.457   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0    8666.0328673.135   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0    8663.2928671.843   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0    8662.0468670.937   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8662.5228669.473   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8664.0628669.473   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8664.5388670.937   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8668.5458671.690   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8667.2118670.920   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0    8667.2118669.380   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0    8668.5458668.610   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8669.8788669.380   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8669.8788670.920   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8669.8778664.759   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8668.5438663.989   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8668.5438662.449   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8669.8778661.679   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8671.2118662.449   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0    8671.2118663.989   0.000  0.00  0.00           O+0
CONECT    1   24   22                                                       
CONECT    2   21                                                            
CONECT    3   20                                                            
CONECT    4    5   19                                                       
CONECT    5    4                                                            
CONECT    6    7   26                                                       
CONECT    7    6   29                                                       
CONECT    8    9   33                                                       
CONECT    9    8                                                            
CONECT   10   30                                                            
CONECT   11   31                                                            
CONECT   12   32                                                            
CONECT   13   23                                                            
CONECT   14   28                                                            
CONECT   15   27                                                            
CONECT   16   17   22                                                       
CONECT   17   16                                                            
CONECT   18   19   22                                                       
CONECT   19   20   18    4                                                  
CONECT   20   19   21    3                                                  
CONECT   21   20   22    2                                                  
CONECT   22   21   18    1   16                                             
CONECT   23   24   28   13                                                  
CONECT   24   23   25    1                                                  
CONECT   25   24   26                                                       
CONECT   26   27   25    6                                                  
CONECT   27   26   28   15                                                  
CONECT   28   23   27   14                                                  
CONECT   29   30   34    7                                                  
CONECT   30   29   31   10                                                  
CONECT   31   30   32   11                                                  
CONECT   32   31   33   12                                                  
CONECT   33   32   34    8                                                  
CONECT   34   29   33                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
beta-D-Fructofuranosyl O-beta-D-glucopyranosyl-(1-6)-alpha-D-glucopyranoside	ChEBI
beta-D-GLCP-(1->6)-alpha-D-GLCP-(12)-beta-D-fruf	ChEBI
b-D-Fructofuranosyl O-b-D-glucopyranosyl-(1-6)-a-D-glucopyranoside	Generator
b-D-GLCP-(1->6)-a-D-GLCP-(12)-b-D-fruf	Generator
beta-D-Fructofuranosyl O-beta-D-glucopyranosyl-(1→6)-alpha-D-glucopyranoside	HMDB
Β-D-fructofuranosyl O-β-D-glucopyranosyl-(1→6)-α-D-glucopyranoside	HMDB
Gentianose	HMDB

Chemical Formula

C₁₈H₃₂O₁₆

Average Mass

504.4380 Da

Monoisotopic Mass

504.16903 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxane-3,4,5-triol

Traditional Name

gentianose

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@](CO)(O[C@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O)[C@@H](O)[C@@H]1O

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/t5-,6-,7-,8-,9-,10-,11+,12+,13-,14-,15+,16-,17-,18+/m1/s1

InChI Key

MUPFEKGTMRGPLJ-WSCXOGSTSA-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
Gentiana algida	LOTUS Database	35616633
Gentiana linearis	LOTUS Database	35616633
Gentiana lutea	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

trisaccharide (CHEBI:28782 )

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	46.77 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

HMDB0034072

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Raffinose

METLIN ID

138

PubChem Compound

117678

PDB ID

Not Available

ChEBI ID

28782

Good Scents ID

Not Available

References

General References

HERISSEY H, WICKSTROM A, COURTOIS JE: [Action of periodic acid on the nonreducing tri- and tetraholosides. II. Study of gentianose]. Bull Soc Chim Biol (Paris). 1951;33(11-12):1768-76. [PubMed:14935697 ]
Keller F, Wiemken A: Differential compartmentation of sucrose and gentianose in the cytosol and vacuoles of storage root protoplasts from Gentiana Lutea L. Plant Cell Rep. 1982 Dec;1(6):274-7. doi: 10.1007/BF00272638. [PubMed:24257774 ]
Tan RX, Wolfender JL, Ma WG, Zhang LX, Hostettmann K: Secoiridoids and antifungal aromatic acids from Gentiana algida. Phytochemistry. 1996 Jan;41(1):111-6. doi: 10.1016/0031-9422(95)00599-4. [PubMed:8588862 ]
LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 (NP0183744)

MOL for NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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 NP0183744 ((2r,3r,4s,5s,6r)-2-{[(2r,3s,4s,5r,6r)-6-{[(2s,3s,4s,5r)-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)