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Showing metabocard for 1,3-Dioxolane (HMDB0244173)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:21:20 UTC
Update Date2021-09-26 22:51:45 UTC
HMDB IDHMDB0244173
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,3-Dioxolane
Description1,3-Dioxolane, also known as formal glycol or dioxolane, belongs to the class of organic compounds known as 1,3-dioxolanes. These are organic compounds containing 1,3-dioxolane, an aliphatic five-member ring with two oxygen atoms in ring positions 1 and 3. Based on a literature review very few articles have been published on 1,3-Dioxolane. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,3-dioxolane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,3-Dioxolane 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0244173 (1,3-Dioxolane)


  Mrv1572004191603472D          

  5  5  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
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3D MOL for HMDB0244173 (1,3-Dioxolane)

HMDB0244173
     RDKit          3D
1,3-Dioxolane
 11 11  0  0  0  0  0  0  0  0999 V2000
   -0.2889    1.0005   -0.2813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9631   -0.2722    0.1925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0436   -0.7772    1.0482 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1476   -0.5913    0.1790 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0736    0.7708   -0.0282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6204    1.8923    0.2772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4353    1.1848   -1.3620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0176   -0.9838   -0.6510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8796   -0.1155    0.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0700   -0.9411    0.6309 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8701   -1.1672   -0.7442 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  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  4 10  1  0
  4 11  1  0
M  END
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3D SDF for HMDB0244173 (1,3-Dioxolane)


  Mrv1572004191603472D          

  5  5  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244173

> <DATABASE_NAME>
hmdb

> <SMILES>
C1COCO1

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O2/c1-2-5-3-4-1/h1-3H2

> <INCHI_KEY>
WNXJIVFYUVYPPR-UHFFFAOYSA-N

> <FORMULA>
C3H6O2

> <MOLECULAR_WEIGHT>
74.079

> <EXACT_MASS>
74.036779433

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
7.1000112734608125

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-dioxolane

> <ALOGPS_LOGP>
-0.61

> <JCHEM_LOGP>
0.016149925666666634

> <ALOGPS_LOGS>
0.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.013397448049778

> <JCHEM_POLAR_SURFACE_AREA>
18.46

> <JCHEM_REFRACTIVITY>
16.8965

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.83e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dioxolane

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0244173 (1,3-Dioxolane)

HMDB0244173
     RDKit          3D
1,3-Dioxolane
 11 11  0  0  0  0  0  0  0  0999 V2000
   -0.2889    1.0005   -0.2813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9631   -0.2722    0.1925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0436   -0.7772    1.0482 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1476   -0.5913    0.1790 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0736    0.7708   -0.0282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6204    1.8923    0.2772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4353    1.1848   -1.3620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0176   -0.9838   -0.6510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8796   -0.1155    0.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0700   -0.9411    0.6309 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8701   -1.1672   -0.7442 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  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  4 10  1  0
  4 11  1  0
M  END
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PDB for HMDB0244173 (1,3-Dioxolane)

HEADER    PROTEIN                                 19-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-16         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    5                                                       
CONECT    3    4    5                                                       
CONECT    4    1    3                                                       
CONECT    5    2    3                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0244173 (1,3-Dioxolane)

COMPND    HMDB0244173
HETATM    1  C1  UNL     1      -0.289   1.001  -0.281  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.963  -0.272   0.192  1.00  0.00           C  
HETATM    3  O1  UNL     1       0.044  -0.777   1.048  1.00  0.00           O  
HETATM    4  C3  UNL     1       1.148  -0.591   0.179  1.00  0.00           C  
HETATM    5  O2  UNL     1       1.074   0.771  -0.028  1.00  0.00           O  
HETATM    6  H1  UNL     1      -0.620   1.892   0.277  1.00  0.00           H  
HETATM    7  H2  UNL     1      -0.435   1.185  -1.362  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.018  -0.984  -0.651  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.880  -0.115   0.739  1.00  0.00           H  
HETATM   10  H5  UNL     1       2.070  -0.941   0.631  1.00  0.00           H  
HETATM   11  H6  UNL     1       0.870  -1.167  -0.744  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    8    9
CONECT    3    4
CONECT    4    5   10   11
END
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SMILES for HMDB0244173 (1,3-Dioxolane)

C1COCO1
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INCHI for HMDB0244173 (1,3-Dioxolane)

InChI=1S/C3H6O2/c1-2-5-3-4-1/h1-3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3-DioxacyclopentaneChEBI
Formal glycolChEBI
Glycol methylene etherChEBI
DioxolaneHMDB
Chemical FormulaC3H6O2
Average Molecular Weight74.079
Monoisotopic Molecular Weight74.036779433
IUPAC Name1,3-dioxolane
Traditional Namedioxolane
CAS Registry NumberNot Available
SMILES
C1COCO1
InChI Identifier
InChI=1S/C3H6O2/c1-2-5-3-4-1/h1-3H2
InChI KeyWNXJIVFYUVYPPR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dioxolanes. These are organic compounds containing 1,3-dioxolane, an aliphatic five-member ring with two oxygen atoms in ring positions 1 and 3.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDioxolanes
Sub Class1,3-dioxolanes
Direct Parent1,3-dioxolanes
Alternative Parents
Substituents
  • Meta-dioxolane
  • Oxacycle
  • Acetal
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
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-0.61ALOGPS
logP0.016ChemAxon
logS0.81ALOGPS
pKa (Strongest Basic)-4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area18.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity16.9 m³·mol⁻¹ChemAxon
Polarizability7.1 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]+124.7830932474
DeepCCS[M-H]-122.88430932474
DeepCCS[M-2H]-158.48130932474
DeepCCS[M+Na]+132.88730932474
AllCCS[M+H]+115.132859911
AllCCS[M+H-H2O]+109.832859911
AllCCS[M+NH4]+120.132859911
AllCCS[M+Na]+121.532859911
AllCCS[M-H]-118.732859911
AllCCS[M+Na-2H]-123.332859911
AllCCS[M+HCOO]-128.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,3-DioxolaneC1COCO1942.6Standard polar33892256
1,3-DioxolaneC1COCO1566.3Standard non polar33892256
1,3-DioxolaneC1COCO1602.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dioxolane GC-MS (Non-derivatized) - 70eV, Positivesplash10-00bc-9000000000-89536a2b6792f257c75d2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dioxolane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 10V, Positive-QTOFsplash10-004i-9000000000-ad3e771fc86b5e98dbb12016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 20V, Positive-QTOFsplash10-004i-9000000000-153cc3e8725585f533e02016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 40V, Positive-QTOFsplash10-004i-9000000000-452517d9177f1c3a28f82016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 10V, Negative-QTOFsplash10-00di-9000000000-3b630efacc79316b85152016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 20V, Negative-QTOFsplash10-00di-9000000000-e1f32d9cdeb7cb5330c52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 40V, Negative-QTOFsplash10-0adi-9000000000-b10ab0daa14edb37f12c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 10V, Positive-QTOFsplash10-0002-9000000000-dca71c83c6eb57cfa1cf2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 20V, Positive-QTOFsplash10-0002-9000000000-60754788b6af33ae13332021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 40V, Positive-QTOFsplash10-052b-9000000000-524c0e0bef7eccfa9d5a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 10V, Negative-QTOFsplash10-0006-9000000000-8e8bc71f32d57847d9a32021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 20V, Negative-QTOFsplash10-0ab9-9000000000-8b70c822c16c182f58542021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dioxolane 40V, Negative-QTOFsplash10-0006-9000000000-33486a1d4b70de2313312021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart 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 IDC00054159
Chemspider ID12066
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDioxolane
METLIN IDNot Available
PubChem Compound12586
PDB IDNot Available
ChEBI ID87597
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1147741
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 ]