NP-MRD: Showing NP-Card for (2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0282336)

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Record Information

Version

2.0

Created at

2022-09-09 09:07:43 UTC

Updated at

2022-09-09 09:07:43 UTC

NP-MRD ID

NP0282336

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

(2R,3R,4S,5R,6R)-2-{[(1S,4S,5R)-4-[(3S)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. (2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Sedum sarmentosum. Based on a literature review very few articles have been published on (2R,3R,4S,5R,6R)-2-{[(1S,4S,5R)-4-[(3S)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309092211072D          

 27 28  0  0  1  0            999 V2000
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 C   0  0  2  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
   -0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -3.3000    0.0000 O   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   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8986   -2.6680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9592   -2.6680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -3.3000    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   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  1  0  0  0
  4 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
  2 21  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
M  END


  Mrv1652309092211072D          

 27 28  0  0  1  0            999 V2000
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 C   0  0  2  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
   -0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -3.3000    0.0000 O   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   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8986   -2.6680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9592   -2.6680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -3.3000    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   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  1  0  0  0
  4 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
  2 21  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0282336

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C19H36O8/c1-10-6-12(7-19(2,3)13(10)5-4-11(22)8-20)26-18-17(25)16(24)15(23)14(9-21)27-18/h10-18,20-25H,4-9H2,1-3H3/t10-,11+,12+,13+,14-,15+,16+,17-,18-/m1/s1

> <INCHI_KEY>
CTTZYKAMCSQZMI-QQBNSDJISA-N

> <FORMULA>
C19H36O8

> <MOLECULAR_WEIGHT>
392.489

> <EXACT_MASS>
392.241018119

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
42.51207834339402

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R,6R)-2-{[(1S,4S,5R)-4-[(3S)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-0.5069140023333323

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.168293369951368

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.206794422064354

> <JCHEM_PKA_STRONGEST_BASIC>
-2.935671303493521

> <JCHEM_POLAR_SURFACE_AREA>
139.84

> <JCHEM_REFRACTIVITY>
96.90289999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R,6R)-2-{[(1S,4S,5R)-4-[(3S)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -8.470   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.334  -8.470   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -4.001  -8.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -6.668  -8.470   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -5.335  -6.160   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.000  -6.160   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.677  -4.980   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.657  -4.980   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335  -6.160   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.002  -6.160   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      10.669  -6.160   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   21                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6   16                                                  
CONECT   16   15                                                            
CONECT   17    4   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18    2   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₃₆O₈

Average Mass

392.4890 Da

Monoisotopic Mass

392.24102 Da

IUPAC Name

(2R,3R,4S,5R,6R)-2-{[(1S,4S,5R)-4-[(3S)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5R,6R)-2-{[(1S,4S,5R)-4-[(3S)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@@H](CC(C)(C)[C@H]1CC[C@H](O)CO)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C19H36O8/c1-10-6-12(7-19(2,3)13(10)5-4-11(22)8-20)26-18-17(25)16(24)15(23)14(9-21)27-18/h10-18,20-25H,4-9H2,1-3H3/t10-,11+,12+,13+,14-,15+,16+,17-,18-/m1/s1

InChI Key

CTTZYKAMCSQZMI-QQBNSDJISA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Sedum sarmentosum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Megastigmane sesquiterpenoid
Sesquiterpenoid
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Oxane
Monosaccharide
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen 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	-0.51	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	139.84 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	96.9 m³·mol⁻¹	ChemAxon
Polarizability	42.51 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

163086255

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,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0282336)

MOL for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0282336 ((2r,3r,4s,5r,6r)-2-{[(1s,4s,5r)-4-[(3s)-3,4-dihydroxybutyl]-3,3,5-trimethylcyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)