NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate (NP0219895)

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Record Information

Version

2.0

Created at

2022-09-05 21:02:18 UTC

Updated at

2022-09-05 21:02:18 UTC

NP-MRD ID

NP0219895

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate

Description

(2S,3R,4S,5S,6R)-6-({[(2R,3S,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate 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. (2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate is found in Coffea arabica. Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-6-({[(2R,3S,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052223022D          

 27 28  0  0  1  0            999 V2000
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  2  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
    5.0013   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.2309   -1.6545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0379   -1.4830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4504   -2.1975    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.1179   -1.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0025   -2.8106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8094   -2.6390    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8984   -2.8106    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.0699   -3.6175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  6  0  0  0
 18 19  1  0  0  0  0
 16 20  1  0  0  0  0
 13 20  1  0  0  0  0
 20 21  1  6  0  0  0
 10 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
  8 26  1  0  0  0  0
 26 27  1  1  0  0  0
M  END


  Mrv1652309052223022D          

 27 28  0  0  1  0            999 V2000
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  2  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
    5.0013   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.2309   -1.6545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0379   -1.4830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4504   -2.1975    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.1179   -1.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0025   -2.8106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8094   -2.6390    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8984   -2.8106    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.0699   -3.6175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  6  0  0  0
 18 19  1  0  0  0  0
 16 20  1  0  0  0  0
 13 20  1  0  0  0  0
 20 21  1  6  0  0  0
 10 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
  8 26  1  0  0  0  0
 26 27  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0219895

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C16H28O11/c1-7(2)3-9(18)27-14-12(21)11(20)10(19)8(26-14)4-24-15-13(22)16(23,5-17)6-25-15/h7-8,10-15,17,19-23H,3-6H2,1-2H3/t8-,10-,11+,12-,13-,14+,15-,16-/m1/s1

> <INCHI_KEY>
ZIEQNJFDWXPCBV-VEVZXMKKSA-N

> <FORMULA>
C16H28O11

> <MOLECULAR_WEIGHT>
396.389

> <EXACT_MASS>
396.163161722

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
38.56825406399311

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.335789259333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.309253381784497

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.700474155746646

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423790163389214

> <JCHEM_POLAR_SURFACE_AREA>
175.37

> <JCHEM_REFRACTIVITY>
85.52160000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-6-({[(2R,3S,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate

> <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  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      13.498  -3.088   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      15.004  -2.768   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.774  -4.102   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      17.020  -3.197   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      16.805  -5.246   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      18.311  -4.926   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      14.744  -5.246   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      15.064  -6.753   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   26                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   22                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   20                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20   16   13   21                                                  
CONECT   21   20                                                            
CONECT   22   10   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    8   27                                                  
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,4S,5S,6R)-6-({[(2R,3S,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoic acid	Generator

Chemical Formula

C₁₆H₂₈O₁₁

Average Mass

396.3890 Da

Monoisotopic Mass

396.16316 Da

IUPAC Name

(2S,3R,4S,5S,6R)-6-({[(2R,3S,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate

Traditional Name

(2S,3R,4S,5S,6R)-6-({[(2R,3S,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C16H28O11/c1-7(2)3-9(18)27-14-12(21)11(20)10(19)8(26-14)4-24-15-13(22)16(23,5-17)6-25-15/h7-8,10-15,17,19-23H,3-6H2,1-2H3/t8-,10-,11+,12-,13-,14+,15-,16-/m1/s1

InChI Key

ZIEQNJFDWXPCBV-VEVZXMKKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Coffea arabica	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
Disaccharide
Glycosyl compound
O-glycosyl compound
Fatty acid ester
Oxane
Tetrahydrofuran
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Primary alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
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	-2.3	ChemAxon
pKa (Strongest Acidic)	11.7	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	175.37 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	85.52 m³·mol⁻¹	ChemAxon
Polarizability	38.57 Å³	ChemAxon
Number of Rings	2	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

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

162879876

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,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate (NP0219895)

MOL for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

3D MOL for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

3D SDF for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

3D-SDF for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

PDB for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

3D PDB for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

SMILES for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

INCHI for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

Structure for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)

3D Structure for NP0219895 ((2s,3r,4s,5s,6r)-6-({[(2r,3s,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl 3-methylbutanoate)