NP-MRD: Showing NP-Card for (2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol (NP0208958)

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Record Information

Version

2.0

Created at

2022-09-05 06:10:53 UTC

Updated at

2022-09-05 06:10:53 UTC

NP-MRD ID

NP0208958

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol

Description

(2S,4R)-4-(beta-D-Glucopyranosyloxy)-2-pentanol 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,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol is found in Crescentia cujete. Based on a literature review very few articles have been published on (2S,4R)-4-(beta-D-Glucopyranosyloxy)-2-pentanol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 40  0  0  0  0  0  0  0  0999 V2000
    4.6618    0.0766   -1.9561 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9469    0.0443   -0.6144 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9285   -1.2879   -0.1845 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5212    0.4630   -0.8693 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6853    0.4758    0.3918 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2807    1.4439    1.3838 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3954    0.8419    0.0166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5544   -0.1302    0.3356 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0896   -0.6024   -0.8081 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4381   -0.7240   -0.8962 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0896    0.5402   -1.3999 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4605    0.4337   -1.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0362   -1.2260    0.3805 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3735   -2.4016    0.7299 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8078   -0.2103    1.4561 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8024    0.7944    1.4124 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4782    0.4452    1.3439 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8485    0.3241    2.6074 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2205    1.0172   -2.1091 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3295   -0.8113   -2.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9190    0.0245   -2.7954 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4472    0.6977    0.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6972   -1.8395   -0.9922 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1007   -0.2279   -1.6276 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5634    1.5197   -1.2311 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6182   -0.5246    0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6507    2.3164    0.7863 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1773    0.9829    1.8327 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5588    1.7549    2.1470 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0053   -0.9778    0.8291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6577   -1.5093   -1.6802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8502    1.4296   -0.8200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6947    0.7171   -2.4353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7477    0.1923   -2.4123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1127   -1.4748    0.2852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5699   -3.1352    0.0710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9702   -0.7271    2.4344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6659    0.3436    1.2439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5501    1.5627    1.1912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9098   -0.6318    2.9214 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  1
  6 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  1
 10 31  1  6
 11 32  1  0
 11 33  1  0
 12 34  1  0
 13 35  1  6
 14 36  1  0
 15 37  1  1
 16 38  1  0
 17 39  1  6
 18 40  1  0
M  END


  Mrv1652309052208102D          

 18 18  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  2  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 O   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  1  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   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
    5.7158   -1.6500    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  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  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
 10 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0208958

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H22O7/c1-5(13)3-6(2)17-11-10(16)9(15)8(14)7(4-12)18-11/h5-16H,3-4H2,1-2H3/t5-,6+,7+,8+,9-,10+,11+/m0/s1

> <INCHI_KEY>
QAHVAJIBDPNFCD-CTPKJSQQSA-N

> <FORMULA>
C11H22O7

> <MOLECULAR_WEIGHT>
266.29

> <EXACT_MASS>
266.136553048

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
27.01263894203749

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.0864049380000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.198479952317836

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210402771789076

> <JCHEM_PKA_STRONGEST_BASIC>
-2.544976649847335

> <JCHEM_POLAR_SURFACE_AREA>
119.61000000000001

> <JCHEM_REFRACTIVITY>
60.6699

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

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

> <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  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+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  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+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      10.669  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   18  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   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    8   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
(2S,4R)-4-(b-D-Glucopyranosyloxy)-2-pentanol	Generator
(2S,4R)-4-(Β-D-glucopyranosyloxy)-2-pentanol	Generator

Chemical Formula

C₁₁H₂₂O₇

Average Mass

266.2900 Da

Monoisotopic Mass

266.13655 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H22O7/c1-5(13)3-6(2)17-11-10(16)9(15)8(14)7(4-12)18-11/h5-16H,3-4H2,1-2H3/t5-,6+,7+,8+,9-,10+,11+/m0/s1

InChI Key

QAHVAJIBDPNFCD-CTPKJSQQSA-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
Crescentia cujete	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
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Secondary alcohol
Acetal
Organoheterocyclic compound
Oxacycle
Polyol
Primary alcohol
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

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

84487494

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101938889

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)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol (NP0208958)

MOL for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

3D MOL for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

3D SDF for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

3D-SDF for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

PDB for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

3D PDB for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

SMILES for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

INCHI for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

Structure for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)

3D Structure for NP0208958 ((2r,3s,4s,5r,6r)-2-(hydroxymethyl)-6-{[(2r,4s)-4-hydroxypentan-2-yl]oxy}oxane-3,4,5-triol)