Hmdb loader

Showing metabocard for Glycidol (HMDB0252861)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 10:57:23 UTC
Update Date2021-09-26 23:05:44 UTC
HMDB IDHMDB0252861
Secondary Accession NumbersNone
Metabolite Identification
Common NameGlycidol
DescriptionGlycidol, also known as oxiranemethanol or epihydrin alcohol, belongs to the class of organic compounds known as epoxides. Epoxides are compounds containing a cyclic ether with three ring atoms(one oxygen and two carbon atoms). Glycidol is an extremely weak basic (essentially neutral) compound (based on its pKa). Glycidol is formally rated as a probable carcinogen (by IARC 2A) and is also a potentially toxic compound. Exposure to glycidol may also cause central nervous system depression, followed by central nervous system stimulation. Glycidol is an organic compound that contains both epoxide and alcohol functional groups. The compound is a slightly viscous liquid that is slightly unstable and is not often encountered in pure form. Being bifunctional, it has a variety of industrial uses. Glycidol is an irritant of the skin, eyes, mucous membranes, and upper respiratory tract. This compound has been identified in human blood as reported by (PMID: 31557052 ). Glycidol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Glycidol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0252861 (Glycidol)


  Mrv0541 08291401542D          

  5  5  0  0  0  0            999 V2000
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
Download

3D MOL for HMDB0252861 (Glycidol)

HMDB0252861
     RDKit          3D
Glycidol
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.7713   -0.1079   -1.0432 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8763   -0.4969   -0.0346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1689    0.5380    0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6081    0.0722    0.1489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305    0.9345   -0.7845 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5118    0.3572   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3920   -1.4327   -0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -0.7618    0.9025 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0358    1.3393    0.9718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3459    0.4977    0.8822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8078   -0.9395   -0.2675 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  3  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
M  END
Download

3D SDF for HMDB0252861 (Glycidol)


  Mrv0541 08291401542D          

  5  5  0  0  0  0            999 V2000
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252861

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1CO1

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2

> <INCHI_KEY>
CTKINSOISVBQLD-UHFFFAOYSA-N

> <FORMULA>
C3H6O2

> <MOLECULAR_WEIGHT>
74.0785

> <EXACT_MASS>
74.036779436

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
7.227893238248548

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxiran-2-ylmethanol

> <ALOGPS_LOGP>
-0.93

> <JCHEM_LOGP>
-0.6773104503333333

> <ALOGPS_LOGS>
1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.602877456783332

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9725014004029697

> <JCHEM_POLAR_SURFACE_AREA>
32.76

> <JCHEM_REFRACTIVITY>
17.006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(+-)-glycidol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0252861 (Glycidol)

HMDB0252861
     RDKit          3D
Glycidol
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.7713   -0.1079   -1.0432 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8763   -0.4969   -0.0346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1689    0.5380    0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6081    0.0722    0.1489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305    0.9345   -0.7845 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5118    0.3572   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3920   -1.4327   -0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -0.7618    0.9025 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0358    1.3393    0.9718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3459    0.4977    0.8822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8078   -0.9395   -0.2675 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  3  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
M  END
Download

PDB for HMDB0252861 (Glycidol)

HEADER    PROTEIN                                 29-AUG-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-AUG-14         0                                  
HETATM    1  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.889   3.969   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -0.325   0.325   0.000  0.00  0.00           O+0
CONECT    1    3    4                                                       
CONECT    2    3    5                                                       
CONECT    3    1    2    5                                                  
CONECT    4    1                                                            
CONECT    5    2    3                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
Download

3D PDB for HMDB0252861 (Glycidol)

COMPND    HMDB0252861
HETATM    1  O1  UNL     1       1.771  -0.108  -1.043  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.876  -0.497  -0.035  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.169   0.538   0.227  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.608   0.072   0.149  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.031   0.935  -0.785  1.00  0.00           O  
HETATM    6  H1  UNL     1       2.512   0.357  -0.579  1.00  0.00           H  
HETATM    7  H2  UNL     1       0.392  -1.433  -0.423  1.00  0.00           H  
HETATM    8  H3  UNL     1       1.374  -0.762   0.902  1.00  0.00           H  
HETATM    9  H4  UNL     1       0.036   1.339   0.972  1.00  0.00           H  
HETATM   10  H5  UNL     1      -2.346   0.498   0.882  1.00  0.00           H  
HETATM   11  H6  UNL     1      -1.808  -0.940  -0.268  1.00  0.00           H  
CONECT    1    2    6
CONECT    2    3    7    8
CONECT    3    4    5    9
CONECT    4    5   10   11
END
Download

SMILES for HMDB0252861 (Glycidol)

OCC1CO1
Download

INCHI for HMDB0252861 (Glycidol)

InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(RS)-3-Hydroxy-1,2-epoxypropaneChEBI
2,3-Epoxy-1-propanolChEBI
3-Hydroxy-1,2-epoxypropaneChEBI
3-Hydroxypropylene oxideChEBI
OxiranemethanolChEBI
Epihydrin alcoholMeSH
Glycidol, (+-)-isomerMeSH
Glycidol, (R)-isomerMeSH
2,3-Epoxypropan-1-olMeSH
2,3-EpoxypropanolMeSH
Chemical FormulaC3H6O2
Average Molecular Weight74.0785
Monoisotopic Molecular Weight74.036779436
IUPAC Nameoxiran-2-ylmethanol
Traditional Name(+-)-glycidol
CAS Registry NumberNot Available
SMILES
OCC1CO1
InChI Identifier
InChI=1S/C3H6O2/c4-1-3-2-5-3/h3-4H,1-2H2
InChI KeyCTKINSOISVBQLD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as epoxides. Epoxides are compounds containing a cyclic ether with three ring atoms(one oxygen and two carbon atoms).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassEpoxides
Sub ClassNot Available
Direct ParentEpoxides
Alternative Parents
Substituents
  • Oxacycle
  • Ether
  • Oxirane
  • Dialkyl ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
Process
Naturally occurring process
RoleNot 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
logP-0.93ALOGPS
logP-0.68ChemAxon
logS1.12ALOGPS
pKa (Strongest Acidic)14.6ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area32.76 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity17.01 m³·mol⁻¹ChemAxon
Polarizability7.23 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+122.63530932474
DeepCCS[M-H]-120.73930932474
DeepCCS[M-2H]-156.12930932474
DeepCCS[M+Na]+130.38830932474
AllCCS[M+H]+118.232859911
AllCCS[M+H-H2O]+113.132859911
AllCCS[M+NH4]+122.932859911
AllCCS[M+Na]+124.232859911
AllCCS[M-H]-119.732859911
AllCCS[M+Na-2H]-124.232859911
AllCCS[M+HCOO]-129.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
GlycidolOCC1CO11596.7Standard polar33892256
GlycidolOCC1CO1701.0Standard non polar33892256
GlycidolOCC1CO1746.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Glycidol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-448d17d594e94cb853c22021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidol GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-0006-9000000000-2d0db93f67aa820a6c8b2014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 10V, Positive-QTOFsplash10-004i-9000000000-cbb771b58d7538f440832016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 20V, Positive-QTOFsplash10-056r-9000000000-8145e330aaa6e9e376552016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 40V, Positive-QTOFsplash10-0a4i-9000000000-58e2f6f1d8d735ac915b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 10V, Negative-QTOFsplash10-00di-9000000000-d19ceca970790fac15112016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 20V, Negative-QTOFsplash10-05fr-9000000000-3f2f9a9bfffd0d2f9f6c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 40V, Negative-QTOFsplash10-0006-9000000000-7126d26f4682a8ca80342016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 10V, Positive-QTOFsplash10-0a4i-9000000000-7508eb6b4830eacd0f4e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 20V, Positive-QTOFsplash10-0a4i-9000000000-086efafc75c2a9f6e6812021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 40V, Positive-QTOFsplash10-052r-9000000000-6297d7489ffbdaa34b422021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 10V, Negative-QTOFsplash10-0ab9-9000000000-b30029d8566d03fb2d862021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 20V, Negative-QTOFsplash10-0ab9-9000000000-64f570cddefe87bf5e332021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidol 40V, Negative-QTOFsplash10-0006-9000000000-ed0ef17f95ec9605443d2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC10920
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGlycidol
METLIN IDNot Available
PubChem Compound11164
PDB IDNot Available
ChEBI ID30966
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]