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Showing NP-Card for 5-Hydroxy-2-benzyl-1,3-dioxane (NP0337065)

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Record Information
Version2.0
Created at2024-09-11 09:07:07 UTC
Updated at2024-09-11 09:07:07 UTC
NP-MRD IDNP0337065
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-Hydroxy-2-benzyl-1,3-dioxane
Description5-Hydroxy-2-benzyl-1,3-dioxane, also known as 2-benzyl-1,3-dioxan-5-ol, belongs to the class of organic compounds known as 1,3-dioxanes. These are organic compounds containing 1,3-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 3. 5-Hydroxy-2-benzyl-1,3-dioxane is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)


  Mrv0541 05061312432D          

 14 15  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   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
    2.8579    3.3000    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
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.9500    0.0000 C   0  0  0  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
    0.0000    5.7750    0.0000 C   0  0  0  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    6.1875    0.0000 O   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
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  7  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 11  1  0  0  0  0
M  END
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3D MOL for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)

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3D SDF for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)

  Mrv0541 05061312432D          

 14 15  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   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
    2.8579    3.3000    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
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.9500    0.0000 C   0  0  0  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
    0.0000    5.7750    0.0000 C   0  0  0  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    6.1875    0.0000 O   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
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  7  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0337065

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1COC(CC2=CC=CC=C2)OC1

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O3/c12-10-7-13-11(14-8-10)6-9-4-2-1-3-5-9/h1-5,10-12H,6-8H2

> <INCHI_KEY>
SCBQUBIXYNMXER-UHFFFAOYSA-N

> <FORMULA>
C11H14O3

> <MOLECULAR_WEIGHT>
194.2271

> <EXACT_MASS>
194.094294314

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
20.53908359088127

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-benzyl-1,3-dioxan-5-ol

> <ALOGPS_LOGP>
1.01

> <JCHEM_LOGP>
1.3860249679999999

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.668730493985223

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3810972819308622

> <JCHEM_POLAR_SURFACE_AREA>
38.69

> <JCHEM_REFRACTIVITY>
52.26510000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-benzyl-1,3-dioxan-5-ol

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)
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PDB for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  10.780   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  11.550   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667  10.780   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    9                                                       
CONECT    5    3    9                                                       
CONECT    6    9   11                                                       
CONECT    7   10   13                                                       
CONECT    8   10   14                                                       
CONECT    9    4    5    6                                                  
CONECT   10    7    8   12                                                  
CONECT   11    6   13   14                                                  
CONECT   12   10                                                            
CONECT   13    7   11                                                       
CONECT   14    8   11                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)
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SMILES for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)
OC1COC(CC2=CC=CC=C2)OC1
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INCHI for NP0337065 (5-Hydroxy-2-benzyl-1,3-dioxane)
InChI=1S/C11H14O3/c12-10-7-13-11(14-8-10)6-9-4-2-1-3-5-9/h1-5,10-12H,6-8H2
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Synonyms
ValueSource
2-(Phenylmethyl)-1,3-dioxan-5-ol, 9ciHMDB
2-Benzyl-1,3-dioxan-5-olHMDB
Chemical FormulaC11H14O3
Average Mass194.2271 Da
Monoisotopic Mass194.09429 Da
IUPAC Name2-benzyl-1,3-dioxan-5-ol
Traditional Name2-benzyl-1,3-dioxan-5-ol
CAS Registry NumberNot Available
SMILES
OC1COC(CC2=CC=CC=C2)OC1
InChI Identifier
InChI=1S/C11H14O3/c12-10-7-13-11(14-8-10)6-9-4-2-1-3-5-9/h1-5,10-12H,6-8H2
InChI KeySCBQUBIXYNMXER-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dioxanes. These are organic compounds containing 1,3-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 3.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassDioxanes  
Sub Class1,3-dioxanes  
Direct Parent1,3-dioxanes  
Alternative Parents
Substituents
  • Benzenoid
    • 

  • Monocyclic benzene moiety
    • 

  • Meta-dioxane
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Acetal
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
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
logP1.01ALOGPS
logP1.39ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)13.67ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area38.69 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.27 m³·mol⁻¹ChemAxon
Polarizability20.54 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041505  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021477  
KNApSAcK IDNot Available
Chemspider ID70841  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound78476  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available