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Showing NP-Card for 2-(hydroxymethyl)oxane-3,4,5-triol (NP0292410)

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Record Information
Version2.0
Created at2022-09-09 23:56:08 UTC
Updated at2022-09-09 23:56:08 UTC
NP-MRD IDNP0292410
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-(hydroxymethyl)oxane-3,4,5-triol
Description 2-(hydroxymethyl)oxane-3,4,5-triol is found in Polygala sibirica and Polygala tenuifolia.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)


  Mrv1533004191522482D          

 11 11  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    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  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.0000    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    0.8250    0.0000 C   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
    2.6842    0.8970    0.6410 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0891   -0.3347    0.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0897   -0.1643   -0.7445 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4434   -1.3258   -1.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5295   -1.7181   -0.1887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5890   -0.6796    0.0658 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3598   -1.0968    1.1487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9700    0.6523    0.4234 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9209    1.6571    0.3639 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1638    1.0058   -0.5034 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3293    1.5155   -1.7037 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6556    1.0453    1.6237 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6172   -0.7613    1.3003 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8441   -1.0738    0.0364 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7177    0.1237   -1.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1331   -2.1119    0.7789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0603   -2.5953   -0.6582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2376   -0.6234   -0.8317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4297   -0.4002    1.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5983    0.5946    1.4583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3436    1.7263   -0.5282 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7501    1.8108    0.0058 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4460    1.8568   -2.2347 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  3  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  6
  5 16  1  0
  5 17  1  0
  6 18  1  6
  7 19  1  0
  8 20  1  1
  9 21  1  0
 10 22  1  1
 11 23  1  0
M  END
Download

3D SDF for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)


  Mrv1533004191522482D          

 11 11  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    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  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.0000    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    0.8250    0.0000 C   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0292410

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OCC(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c7-1-4-6(10)5(9)3(8)2-11-4/h3-10H,1-2H2

> <INCHI_KEY>
MPCAJMNYNOGXPB-UHFFFAOYSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.51101817384558

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-2.62

> <JCHEM_LOGP>
-2.5683152763333332

> <ALOGPS_LOGS>
0.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.620852613832781

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.664170582578826

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9785121292856447

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
34.893499999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)

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PDB for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)
HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   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       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    3   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)
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SMILES for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)
OCC1OCC(O)C(O)C1O
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INCHI for NP0292410 (2-(hydroxymethyl)oxane-3,4,5-triol)
InChI=1S/C6H12O5/c7-1-4-6(10)5(9)3(8)2-11-4/h3-10H,1-2H2
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View in JSmol
Synonyms
ValueSource
1,5-SorbitanMeSH
1-Deoxy-D-glucopyranoseMeSH
1,5-AnhydroglucitolMeSH
1-Deoxy-D-glucoseMeSH
PolygalitolMeSH
1,5-Anhydro-D-sorbitolMeSH
1-DeoxyglucoseMeSH
1,5-Anhydro-D-glucitolMeSH
1,5-AnhydrosorbitolMeSH
AceritolMeSH
Chemical FormulaC6H12O5
Average Mass164.1570 Da
Monoisotopic Mass164.06847 Da
IUPAC Name2-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
OCC1OCC(O)C(O)C1O
InChI Identifier
InChI=1S/C6H12O5/c7-1-4-6(10)5(9)3(8)2-11-4/h3-10H,1-2H2
InChI KeyMPCAJMNYNOGXPB-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Polygala sibiricaLOTUS Database
Polygala tenuifoliaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentMonosaccharides  
Alternative Parents
Substituents
  • Oxane
    • 

  • Monosaccharide
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.6ALOGPS
logP-2.6ChemAxon
logS0.8ALOGPS
pKa (Strongest Acidic)12.66ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity34.89 m³·mol⁻¹ChemAxon
Polarizability15.51 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030193  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound219984  
PDB IDNot Available
ChEBI ID144042  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]