NP-MRD: Showing NP-Card for (2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol (NP0300953)

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Record Information

Version

2.0

Created at

2022-09-10 13:38:23 UTC

Updated at

2022-09-10 13:38:23 UTC

NP-MRD ID

NP0300953

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol

Description

(2S,3R,4R,5R,6R)-2-methyl-6-{[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{[(2E)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}oxan-2-yl]methoxy}oxane-3,4,5-triol belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol. (2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol is found in Rodgersia sambucifolia. Based on a literature review very few articles have been published on (2S,3R,4R,5R,6R)-2-methyl-6-{[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{[(2E)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}oxan-2-yl]methoxy}oxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102215382D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309102215382D          

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 19 20  1  1  0  0  0
  8 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
  6 25  1  0  0  0  0
 25 26  1  1  0  0  0
  2 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0300953

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@@H](OC[C@H]2O[C@@H](OC\C=C(/C)CCCC(C)(C)O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C22H40O11/c1-11(6-5-8-22(3,4)29)7-9-30-20-19(28)17(26)15(24)13(33-20)10-31-21-18(27)16(25)14(23)12(2)32-21/h7,12-21,23-29H,5-6,8-10H2,1-4H3/b11-7+/t12-,13+,14-,15+,16+,17-,18+,19+,20+,21+/m0/s1

> <INCHI_KEY>
DIQXCEDSXBEWCQ-ANSYQZRDSA-N

> <FORMULA>
C22H40O11

> <MOLECULAR_WEIGHT>
480.551

> <EXACT_MASS>
480.257062108

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
51.20756537375421

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(2E)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-1.0579132323333338

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.44430188552365

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.917395800647098

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2204234064639432

> <JCHEM_POLAR_SURFACE_AREA>
178.53

> <JCHEM_REFRACTIVITY>
115.45110000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(2E)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002 -12.320   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.335 -13.860   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.667 -12.320   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001   5.390   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.437   3.286   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.897   5.954   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   27                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   21                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   11   20                                                  
CONECT   20   19                                                            
CONECT   21    8   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    6   26                                                  
CONECT   26   25                                                            
CONECT   27    2   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32   33                                             
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   30                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₄₀O₁₁

Average Mass

480.5510 Da

Monoisotopic Mass

480.25706 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-{[(2E)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5S,6R)-2-{[(2E)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](OC[C@H]2O[C@@H](OC\C=C(/C)CCCC(C)(C)O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C22H40O11/c1-11(6-5-8-22(3,4)29)7-9-30-20-19(28)17(26)15(24)13(33-20)10-31-21-18(27)16(25)14(23)12(2)32-21/h7,12-21,23-29H,5-6,8-10H2,1-4H3/b11-7+/t12-,13+,14-,15+,16+,17-,18+,19+,20+,21+/m0/s1

InChI Key

DIQXCEDSXBEWCQ-ANSYQZRDSA-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
Rodgersia sambucifolia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl glycosides

Direct Parent

Fatty acyl glycosides of mono- and disaccharides

Alternative Parents

Substituents

Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Disaccharide
Glycosyl compound
O-glycosyl compound
Oxane
Tertiary alcohol
Secondary alcohol
Acetal
Organoheterocyclic compound
Oxacycle
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
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	-1.1	ChemAxon
pKa (Strongest Acidic)	11.92	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	178.53 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	115.45 m³·mol⁻¹	ChemAxon
Polarizability	51.21 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

162994279

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol (NP0300953)

MOL for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

3D MOL for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

3D SDF for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

3D-SDF for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

PDB for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

3D PDB for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

SMILES for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

INCHI for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

Structure for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)

3D Structure for NP0300953 ((2r,3r,4s,5s,6r)-2-{[(2e)-7-hydroxy-3,7-dimethyloct-2-en-1-yl]oxy}-6-({[(2r,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxane-3,4,5-triol)