NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate (NP0326020)

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Record Information

Version

2.0

Created at

2022-09-12 07:13:21 UTC

Updated at

2022-09-12 07:13:21 UTC

NP-MRD ID

NP0326020

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate

Description

6-O-[(S)-2-Methylene-3,4-dihydroxybutanoyl]-beta-D-glucopyranose belongs to the class of organic compounds known as saccharolipids. Saccharolipids are compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a sugar substitutes for the glycerol backbone that is present in glycerolipids and glycerophospholipids. The most familiar saccharolipids contain an acylated glucosamine. In contrast to others glycolipids, the fatty acid is not glycosidically linked to the sugar moiety. [(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate is found in Tulipa gesneriana and Tulipa sylvestris. Based on a literature review very few articles have been published on 6-O-[(S)-2-Methylene-3,4-dihydroxybutanoyl]-beta-D-glucopyranose.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309122209132D          

 20 20  0  0  1  0            999 V2000
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  1  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
   -2.1434   -2.8875    0.0000 C   0  0  1  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 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  6  0  0  0
  2 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0326020

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H18O9/c1-4(5(13)2-12)10(17)19-3-6-7(14)8(15)9(16)11(18)20-6/h5-9,11-16,18H,1-3H2/t5-,6-,7-,8+,9-,11-/m1/s1

> <INCHI_KEY>
FMHJNIRDGYFPEC-XYLHZXCYSA-N

> <FORMULA>
C11H18O9

> <MOLECULAR_WEIGHT>
294.256

> <EXACT_MASS>
294.09508216

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
27.598388129303324

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6R)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3S)-3,4-dihydroxy-2-methylidenebutanoate

> <JCHEM_LOGP>
-3.0173430766666662

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.63600367632716

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.295757534756236

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9670816840423626

> <JCHEM_POLAR_SURFACE_AREA>
156.91

> <JCHEM_REFRACTIVITY>
61.81689999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6R)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3S)-3,4-dihydroxy-2-methylidenebutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    7   16                                                  
CONECT   16   15                                                            
CONECT   17    2   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
6-O-[(S)-2-Methylene-3,4-dihydroxybutanoyl]-b-D-glucopyranose	Generator
6-O-[(S)-2-Methylene-3,4-dihydroxybutanoyl]-β-D-glucopyranose	Generator

Chemical Formula

C₁₁H₁₈O₉

Average Mass

294.2560 Da

Monoisotopic Mass

294.09508 Da

IUPAC Name

[(2R,3S,4S,5R,6R)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3S)-3,4-dihydroxy-2-methylidenebutanoate

Traditional Name

[(2R,3S,4S,5R,6R)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3S)-3,4-dihydroxy-2-methylidenebutanoate

CAS Registry Number

Not Available

SMILES

OC[C@@H](O)C(=C)C(=O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C11H18O9/c1-4(5(13)2-12)10(17)19-3-6-7(14)8(15)9(16)11(18)20-6/h5-9,11-16,18H,1-3H2/t5-,6-,7-,8+,9-,11-/m1/s1

InChI Key

FMHJNIRDGYFPEC-XYLHZXCYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Tulipa gesneriana	LOTUS Database	35616633
Tulipa sylvestris	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as saccharolipids. Saccharolipids are compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a sugar substitutes for the glycerol backbone that is present in glycerolipids and glycerophospholipids. The most familiar saccharolipids contain an acylated glucosamine. In contrast to others glycolipids, the fatty acid is not glycosidically linked to the sugar moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Saccharolipids

Sub Class

Not Available

Direct Parent

Saccharolipids

Alternative Parents

Substituents

Saccharolipid
Beta-hydroxy acid
Fatty acid ester
Hydroxy acid
Monosaccharide
Fatty acyl
Oxane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
1,2-diol
Carboxylic acid ester
Hemiacetal
Secondary alcohol
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organoheterocyclic compound
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Primary alcohol
Organic oxygen compound
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	-3	ChemAxon
pKa (Strongest Acidic)	11.3	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	156.91 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	61.82 m³·mol⁻¹	ChemAxon
Polarizability	27.6 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

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

24939251

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate (NP0326020)

MOL for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

3D MOL for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

3D SDF for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

3D-SDF for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

PDB for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

3D PDB for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

SMILES for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

INCHI for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

Structure for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)

3D Structure for NP0326020 ([(2r,3s,4s,5r,6r)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl (3s)-3,4-dihydroxy-2-methylidenebutanoate)