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Showing metabocard for 3-Isoxazolidinone (HMDB0039426)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:53:24 UTC
Update Date2023-02-21 17:26:56 UTC
HMDB IDHMDB0039426
Secondary Accession Numbers
  • HMDB39426
Metabolite Identification
Common Name3-Isoxazolidinone
Description3-Isoxazolidinone belongs to the class of organic compounds known as oxazolidinones. Oxazolidinones are compounds containing an oxazolidinone moiety, which is an oxazolidine bearing a ketone group. 3-Isoxazolidinone has been detected, but not quantified in, pulses. This could make 3-isoxazolidinone a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 3-Isoxazolidinone.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039426 (3-Isoxazolidinone)


  Mrv0541 08271307332D          

  6  6  0  0  0  0            999 V2000
    0.0000    1.2169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.3919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674   -0.0930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.8777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.8777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.0930    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  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
M  END
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3D MOL for HMDB0039426 (3-Isoxazolidinone)

HMDB0039426
     RDKit          3D
3-Isoxazolidinone
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.8844    1.4744   -0.1795 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    0.6376   -0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5121    0.8076   -0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9755   -0.5507    0.2832 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0184   -1.3755   -0.3133 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1794   -0.7689   -0.1281 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7991    1.6154    0.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8284    0.9695   -1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9684   -0.8238   -0.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9891   -0.6668    1.3903 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0579   -1.3187    0.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  6 11  1  0
M  END
Download

3D SDF for HMDB0039426 (3-Isoxazolidinone)


  Mrv0541 08271307332D          

  6  6  0  0  0  0            999 V2000
    0.0000    1.2169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.3919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674   -0.0930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.8777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.8777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.0930    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  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
M  END
> <DATABASE_ID>
HMDB0039426

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCON1

> <INCHI_IDENTIFIER>
InChI=1S/C3H5NO2/c5-3-1-2-6-4-3/h1-2H2,(H,4,5)

> <INCHI_KEY>
QXDOFVVNXBGLKK-UHFFFAOYSA-N

> <FORMULA>
C3H5NO2

> <MOLECULAR_WEIGHT>
87.0773

> <EXACT_MASS>
87.032028409

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
7.607220949027831

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2-oxazolidin-3-one

> <ALOGPS_LOGP>
-1.54

> <JCHEM_LOGP>
-0.7171675736666667

> <ALOGPS_LOGS>
0.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.455380866118047

> <JCHEM_PKA_STRONGEST_BASIC>
-4.618021479813882

> <JCHEM_POLAR_SURFACE_AREA>
38.33

> <JCHEM_REFRACTIVITY>
18.8531

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2-oxazolidin-3-one

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0039426 (3-Isoxazolidinone)

HMDB0039426
     RDKit          3D
3-Isoxazolidinone
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.8844    1.4744   -0.1795 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    0.6376   -0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5121    0.8076   -0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9755   -0.5507    0.2832 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0184   -1.3755   -0.3133 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1794   -0.7689   -0.1281 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7991    1.6154    0.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8284    0.9695   -1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9684   -0.8238   -0.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9891   -0.6668    1.3903 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0579   -1.3187    0.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  6 11  1  0
M  END
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PDB for HMDB0039426 (3-Isoxazolidinone)

HEADER    PROTEIN                                 27-AUG-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-AUG-13         0                                  
HETATM    1  O   UNK     0       0.000   2.272   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.000   0.732   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.246  -0.174   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770  -1.638   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.770  -1.638   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -1.246  -0.174   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    2    5                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0039426 (3-Isoxazolidinone)

COMPND    HMDB0039426
HETATM    1  O1  UNL     1       1.884   1.474  -0.179  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.969   0.638  -0.155  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.512   0.808  -0.146  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.976  -0.551   0.283  1.00  0.00           C  
HETATM    5  O2  UNL     1      -0.018  -1.376  -0.313  1.00  0.00           O  
HETATM    6  N1  UNL     1       1.179  -0.769  -0.128  1.00  0.00           N  
HETATM    7  H1  UNL     1      -0.799   1.615   0.548  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.828   0.970  -1.180  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.968  -0.824  -0.124  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.989  -0.667   1.390  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.058  -1.319   0.004  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    7    8
CONECT    4    5    9   10
CONECT    5    6
CONECT    6   11
END
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SMILES for HMDB0039426 (3-Isoxazolidinone)

O=C1CCON1
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INCHI for HMDB0039426 (3-Isoxazolidinone)

InChI=1S/C3H5NO2/c5-3-1-2-6-4-3/h1-2H2,(H,4,5)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-IsoxazolidoneHMDB, MeSH
Chemical FormulaC3H5NO2
Average Molecular Weight87.0773
Monoisotopic Molecular Weight87.032028409
IUPAC Name1,2-oxazolidin-3-one
Traditional Name1,2-oxazolidin-3-one
CAS Registry Number1192-07-0
SMILES
O=C1CCON1
InChI Identifier
InChI=1S/C3H5NO2/c5-3-1-2-6-4-3/h1-2H2,(H,4,5)
InChI KeyQXDOFVVNXBGLKK-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxazolidinones. Oxazolidinones are compounds containing an oxazolidinone moiety, which is an oxazolidine bearing a ketone group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolidines
Sub ClassOxazolidines
Direct ParentOxazolidinones
Alternative Parents
Substituents
  • Oxazolidinone
  • Isoxazolidine
  • Oxacycle
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point70 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility739 g/LALOGPS
logP-1.5ALOGPS
logP-0.72ChemAxon
logS0.93ALOGPS
pKa (Strongest Acidic)8.46ChemAxon
pKa (Strongest Basic)-4.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area38.33 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity18.85 m³·mol⁻¹ChemAxon
Polarizability7.61 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
DarkChem[M+H]+115.09431661259
DarkChem[M-H]-107.77231661259
DeepCCS[M+H]+123.27330932474
DeepCCS[M-H]-121.29530932474
DeepCCS[M-2H]-157.09730932474
DeepCCS[M+Na]+131.50330932474
AllCCS[M+H]+118.632859911
AllCCS[M+H-H2O]+113.432859911
AllCCS[M+NH4]+123.432859911
AllCCS[M+Na]+124.832859911
AllCCS[M-H]-116.432859911
AllCCS[M+Na-2H]-120.232859911
AllCCS[M+HCOO]-124.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-IsoxazolidinoneO=C1CCON11730.2Standard polar33892256
3-IsoxazolidinoneO=C1CCON1924.0Standard non polar33892256
3-IsoxazolidinoneO=C1CCON11094.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Isoxazolidinone,1TMS,isomer #1C[Si](C)(C)N1OCCC1=O1246.6Semi standard non polar33892256
3-Isoxazolidinone,1TMS,isomer #1C[Si](C)(C)N1OCCC1=O1128.4Standard non polar33892256
3-Isoxazolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1OCCC1=O1389.2Semi standard non polar33892256
3-Isoxazolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1OCCC1=O1383.1Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Isoxazolidinone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a70-9000000000-92a5ba6e55e79b5ed7822017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Isoxazolidinone 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 - 3-Isoxazolidinone 10V, Positive-QTOFsplash10-000i-9000000000-ed1a0e00d8f856596fbe2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 20V, Positive-QTOFsplash10-0079-9000000000-d978304c636a737a1b182016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 40V, Positive-QTOFsplash10-0ab9-9000000000-8c1feff6ab020a20473f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 10V, Negative-QTOFsplash10-000i-9000000000-f64ab5ae8c845d8807842016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 20V, Negative-QTOFsplash10-000i-9000000000-f728ae983446322207c82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 40V, Negative-QTOFsplash10-0006-9000000000-3346f658351ec6abbec92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 10V, Negative-QTOFsplash10-000f-9000000000-564f3689da94fe061a882021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 20V, Negative-QTOFsplash10-0006-9000000000-e77ad3c8cd299b9aa1582021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 40V, Negative-QTOFsplash10-0006-9000000000-1ad02c1fe05d35273ee92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 10V, Positive-QTOFsplash10-000i-9000000000-c5b0ec37489f25ccc63f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 20V, Positive-QTOFsplash10-000i-9000000000-f8913d6759128ef7e1ed2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Isoxazolidinone 40V, Positive-QTOFsplash10-0006-9000000000-e15a678110a9e36b61182021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019020
KNApSAcK IDC00055275
Chemspider ID167255
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound192737
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .