NP-MRD: Showing NP-Card for Clusianose (NP0050644)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-27 22:00:16 UTC

Updated at

2022-04-27 22:00:16 UTC

NP-MRD ID

NP0050644

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Clusianose

Description

(2R,3R,4R)-2-({[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)pentane-1,2,3,4,5-pentol belongs to the class of organic compounds known as glycosylglycerols. These are glycerolipids structurally characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage. Clusianose is found in Primula clusiana, Primula glaucescens, Primula integrifolia and Primula spp.. Based on a literature review very few articles have been published on (2R,3R,4R)-2-({[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)pentane-1,2,3,4,5-pentol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200002D          

 23 23  0  0  1  0            999 V2000
    0.0000    3.3000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    4.1250    0.0000 C   0  0  1  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    4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.5855    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
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  1  0  0  0
  1  8  1  6  0  0  0
  1  9  1  1  0  0  0
  9 10  1  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  6  0  0  0
 15 18  1  6  0  0  0
 14 19  1  6  0  0  0
 13 20  1  6  0  0  0
 20 21  1  0  0  0  0
  1 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050644

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H24O11/c13-1-5(16)10(20)12(21,3-15)4-22-11-9(19)8(18)7(17)6(2-14)23-11/h5-11,13-21H,1-4H2/t5-,6-,7+,8+,9+,10-,11-,12-/m1/s1

> <INCHI_KEY>
KMBKXANDSFBRCO-BCOZIXHUSA-N

> <FORMULA>
C12H24O11

> <MOLECULAR_WEIGHT>
344.313

> <EXACT_MASS>
344.131861593

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
31.574573198611688

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-2-({[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)pentane-1,2,3,4,5-pentol

> <ALOGPS_LOGP>
-3.03

> <JCHEM_LOGP>
-5.636852850666665

> <ALOGPS_LOGS>
-0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.406045878650815

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.864363714071144

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810834237083093

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
71.0363

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.73e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R)-2-({[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)pentane-1,2,3,4,5-pentol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   7.700   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.667   7.700   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334  10.010   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.667  10.780   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.540   6.160   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.540   6.160   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.310   4.826   0.000  0.00  0.00           O+0
CONECT    1    2    8    9   22                                             
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5                                                            
CONECT    7    2                                                            
CONECT    8    1                                                            
CONECT    9    1   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   15                                                            
CONECT   19   14                                                            
CONECT   20   13   21                                                       
CONECT   21   20                                                            
CONECT   22    1   23                                                       
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₄O₁₁

Average Mass

344.3130 Da

Monoisotopic Mass

344.13186 Da

IUPAC Name

(2R,3R,4R)-2-({[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)pentane-1,2,3,4,5-pentol

Traditional Name

(2R,3R,4R)-2-({[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)pentane-1,2,3,4,5-pentol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C12H24O11/c13-1-5(16)10(20)12(21,3-15)4-22-11-9(19)8(18)7(17)6(2-14)23-11/h5-11,13-21H,1-4H2/t5-,6-,7+,8+,9+,10-,11-,12-/m1/s1

InChI Key

KMBKXANDSFBRCO-BCOZIXHUSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Primula clusiana	Plant	KNApSAcK
Primula glaucescens	Plant	KNApSAcK
Primula integrifolia	Plant	KNApSAcK
Primula spp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylglycerols. These are glycerolipids structurally characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerolipids

Sub Class

Glycosylglycerols

Direct Parent

Glycosylglycerols

Alternative Parents

Substituents

Glycosylglycerol
Fatty acyl glycoside of mono- or disaccharide
Fatty acyl glycoside
Hexose monosaccharide
Alkyl glycoside
O-glycosyl compound
Glycosyl compound
Fatty acyl
Sugar alcohol
Oxane
Monosaccharide
Tertiary alcohol
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	-3	ALOGPS
logP	-5.6	ChemAxon
logS	-0.1	ALOGPS
pKa (Strongest Acidic)	11.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	200.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	71.04 m³·mol⁻¹	ChemAxon
Polarizability	31.57 Å³	ChemAxon
Number of Rings	1	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

162944522

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Clusianose (NP0050644)

MOL for NP0050644 (Clusianose)

3D MOL for NP0050644 (Clusianose)

3D SDF for NP0050644 (Clusianose)

3D-SDF for NP0050644 (Clusianose)

PDB for NP0050644 (Clusianose)

3D PDB for NP0050644 (Clusianose)

SMILES for NP0050644 (Clusianose)

INCHI for NP0050644 (Clusianose)

Structure for NP0050644 (Clusianose)

3D Structure for NP0050644 (Clusianose)