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Showing metabocard for (2S,3S)-(-)-3-Phenylglycidol (HMDB0341207)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:42:02 UTC
Update Date2022-09-22 18:34:39 UTC
HMDB IDHMDB0341207
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2S,3S)-(-)-3-Phenylglycidol
Description(2S,3S)-(-)-3-Phenylglycidol belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene. Based on a literature review a small amount of articles have been published on (2S,3S)-(-)-3-Phenylglycidol.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)


  Mrv1652309092222202D          

 13 14  0  0  1  0            999 V2000
   -0.0824   -1.0240    0.0000 H   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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -1.9520    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2814   -1.3686    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -3.6020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  6  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  1  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
M  END
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3D MOL for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)

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3D SDF for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)

  Mrv1652309092222202D          

 13 14  0  0  1  0            999 V2000
   -0.0824   -1.0240    0.0000 H   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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -1.9520    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2814   -1.3686    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -3.6020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  6  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  1  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341207

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]1(CO)O[C@@]1([H])C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H10O2/c10-6-8-9(11-8)7-4-2-1-3-5-7/h1-5,8-10H,6H2/t8-,9-/m0/s1

> <INCHI_KEY>
PVALSANGMFRTQM-IUCAKERBSA-N

> <FORMULA>
C9H10O2

> <MOLECULAR_WEIGHT>
150.177

> <EXACT_MASS>
150.068079562

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
16.02685511659535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S,3S)-3-phenyloxiran-2-yl]methanol

> <JCHEM_LOGP>
1.1069297369999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.579991402942014

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9825117603531623

> <JCHEM_POLAR_SURFACE_AREA>
32.76

> <JCHEM_REFRACTIVITY>
41.28880000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3S)-3-phenyloxiran-2-yl]methanol

> <JCHEM_VEBER_RULE>
1

$$$$

Download
3D-SDF for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)
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PDB for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)
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  H   UNK     0      -0.154  -1.911   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.104  -3.644   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.564  -3.644   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0      -0.525  -2.555   0.000  0.00  0.00           H+0
HETATM    8  C   UNK     0      -0.770  -4.414   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.770  -5.954   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.104  -6.724   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.437  -5.954   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.437  -4.414   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.104  -3.644   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    5    6                                             
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    2    7    8                                             
CONECT    7    6                                                            
CONECT    8    6    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

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3D PDB for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)
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SMILES for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)
[H][C@@]1(CO)O[C@@]1([H])C1=CC=CC=C1
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INCHI for HMDB0341207 ((2S,3S)-(-)-3-Phenylglycidol)
InChI=1S/C9H10O2/c10-6-8-9(11-8)7-4-2-1-3-5-7/h1-5,8-10H,6H2/t8-,9-/m0/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC9H10O2
Average Molecular Weight150.177
Monoisotopic Molecular Weight150.068079562
IUPAC Name[(2S,3S)-3-phenyloxiran-2-yl]methanol
Traditional Name[(2S,3S)-3-phenyloxiran-2-yl]methanol
CAS Registry NumberNot Available
SMILES
[H][C@@]1(CO)O[C@@]1([H])C1=CC=CC=C1
InChI Identifier
InChI=1S/C9H10O2/c10-6-8-9(11-8)7-4-2-1-3-5-7/h1-5,8-10H,6H2/t8-,9-/m0/s1
InChI KeyPVALSANGMFRTQM-IUCAKERBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.
KingdomOrganic compounds  
Super ClassBenzenoids  
ClassBenzene and substituted derivatives  
Sub ClassNot Available
Direct ParentBenzene and substituted derivatives  
Alternative Parents
Substituents
  • Monocyclic benzene moiety
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Ether
    • 

  • Oxirane
    • 

  • Dialkyl ether
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.11ChemAxon
pKa (Strongest Acidic)14.58ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area32.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity41.29 m³·mol⁻¹ChemAxon
Polarizability16.03 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID131532  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound149229  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]