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Showing metabocard for 2-Oxazolidinone (HMDB0245282)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:22:11 UTC
Update Date2021-09-26 22:53:40 UTC
HMDB IDHMDB0245282
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Oxazolidinone
Descriptionoxazolidin-2-one belongs to the class of organic compounds known as oxazolines. These are organic compounds containing 1,3-oxazoline, a five-membered ring with a nitrogen and an oxygen atoms at the 1- and 3-position, respectively. Additionally, it contains two double bonds. oxazolidin-2-one is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on oxazolidin-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-oxazolidinone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Oxazolidinone 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 HMDB0245282 (2-Oxazolidinone)


  Mrv1652309112100222D          

  6  6  0  0  0  0            999 V2000
    0.9803   -0.1553    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
   -0.0997    0.6294    0.0000 O   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
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
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3D MOL for HMDB0245282 (2-Oxazolidinone)

HMDB0245282
     RDKit          3D
2-Oxazolidinone
 11 11  0  0  0  0  0  0  0  0999 V2000
    2.6359    0.6238   -0.0807 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3950    0.3974    0.0247 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7255   -0.8576   -0.0419 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6542   -0.5691   -0.3913 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8637    0.7303    0.3633 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4024    1.3471    0.2323 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1482   -1.7877    0.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3537   -1.3604   -0.0691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6931   -0.3570   -1.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6723    1.2979   -0.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0700    0.5352    1.4245 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
  4  8  1  0
  4  9  1  0
  5 10  1  0
  5 11  1  0
M  END
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3D SDF for HMDB0245282 (2-Oxazolidinone)


  Mrv1652309112100222D          

  6  6  0  0  0  0            999 V2000
    0.9803   -0.1553    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
   -0.0997    0.6294    0.0000 O   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
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245282

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1NCCO1

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

> <INCHI_KEY>
IZXIZTKNFFYFOF-UHFFFAOYSA-N

> <FORMULA>
C3H5NO2

> <MOLECULAR_WEIGHT>
87.078

> <EXACT_MASS>
87.032028405

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
7.634759889906261

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-0.35884606966666666

> <ALOGPS_LOGS>
0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.993693106174945

> <JCHEM_POLAR_SURFACE_AREA>
38.33

> <JCHEM_REFRACTIVITY>
19.0172

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
oxazolidinone

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0245282 (2-Oxazolidinone)

HMDB0245282
     RDKit          3D
2-Oxazolidinone
 11 11  0  0  0  0  0  0  0  0999 V2000
    2.6359    0.6238   -0.0807 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3950    0.3974    0.0247 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7255   -0.8576   -0.0419 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6542   -0.5691   -0.3913 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8637    0.7303    0.3633 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4024    1.3471    0.2323 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1482   -1.7877    0.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3537   -1.3604   -0.0691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6931   -0.3570   -1.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6723    1.2979   -0.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0700    0.5352    1.4245 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
  4  8  1  0
  4  9  1  0
  5 10  1  0
  5 11  1  0
M  END
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PDB for HMDB0245282 (2-Oxazolidinone)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    1                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0245282 (2-Oxazolidinone)

COMPND    HMDB0245282
HETATM    1  O1  UNL     1       2.636   0.624  -0.081  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.395   0.397   0.025  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.726  -0.858  -0.042  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.654  -0.569  -0.391  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.864   0.730   0.363  1.00  0.00           C  
HETATM    6  O2  UNL     1       0.402   1.347   0.232  1.00  0.00           O  
HETATM    7  H1  UNL     1       1.148  -1.788   0.127  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.354  -1.360  -0.069  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.693  -0.357  -1.470  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.672   1.298  -0.119  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.070   0.535   1.425  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    7
CONECT    4    5    8    9
CONECT    5    6   10   11
END
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SMILES for HMDB0245282 (2-Oxazolidinone)

O=C1NCCO1
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INCHI for HMDB0245282 (2-Oxazolidinone)

InChI=1S/C3H5NO2/c5-3-4-1-2-6-3/h1-2H2,(H,4,5)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3 Oxazolidin 2 oneMeSH
1,3 Oxazolidine 2 oneMeSH
1,3-Oxazolidin-2-oneMeSH
1,3-Oxazolidine-2-oneMeSH
2 OxazolidoneMeSH
2 OxazolidinoneMeSH
2-OxazolidoneMeSH
Oxazolidin 2 oneMeSH
OxazolidinoneMeSH
OxazolidinonesMeSH
Oxazolidin-2-oneMeSH
Chemical FormulaC3H5NO2
Average Molecular Weight87.078
Monoisotopic Molecular Weight87.032028405
IUPAC Name1,3-oxazolidin-2-one
Traditional Nameoxazolidinone
CAS Registry NumberNot Available
SMILES
O=C1NCCO1
InChI Identifier
InChI=1S/C3H5NO2/c5-3-4-1-2-6-3/h1-2H2,(H,4,5)
InChI KeyIZXIZTKNFFYFOF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxazolines. These are organic compounds containing 1,3-oxazoline, a five-membered ring with a nitrogen and an oxygen atoms at the 1- and 3-position, respectively. Additionally, it contains two double bonds.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolines
Sub ClassOxazolines
Direct ParentOxazolines
Alternative Parents
Substituents
  • Oxazoline
  • Oxacycle
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen 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-1.6ALOGPS
logP-0.36ChemAxon
logS0.89ALOGPS
pKa (Strongest Acidic)12.99ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area38.33 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity19.02 m³·mol⁻¹ChemAxon
Polarizability7.63 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]+124.0430932474
DeepCCS[M-H]-122.13130932474
DeepCCS[M-2H]-157.61830932474
DeepCCS[M+Na]+132.17330932474
AllCCS[M+H]+118.932859911
AllCCS[M+H-H2O]+113.832859911
AllCCS[M+NH4]+123.732859911
AllCCS[M+Na]+125.132859911
AllCCS[M-H]-117.032859911
AllCCS[M+Na-2H]-120.832859911
AllCCS[M+HCOO]-125.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-OxazolidinoneO=C1NCCO12206.4Standard polar33892256
2-OxazolidinoneO=C1NCCO11015.3Standard non polar33892256
2-OxazolidinoneO=C1NCCO11176.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Oxazolidinone,1TMS,isomer #1C[Si](C)(C)N1CCOC1=O1179.7Semi standard non polar33892256
2-Oxazolidinone,1TMS,isomer #1C[Si](C)(C)N1CCOC1=O1141.9Standard non polar33892256
2-Oxazolidinone,1TMS,isomer #1C[Si](C)(C)N1CCOC1=O1682.3Standard polar33892256
2-Oxazolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCOC1=O1402.9Semi standard non polar33892256
2-Oxazolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCOC1=O1413.8Standard non polar33892256
2-Oxazolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCOC1=O1834.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Oxazolidinone GC-MS (Non-derivatized) - 70eV, Positivesplash10-002o-9000000000-ecfed8aee9ba3ec8fdb72021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Oxazolidinone 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 - 2-Oxazolidinone 10V, Positive-QTOFsplash10-000i-9000000000-413d887f5921b027d58a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Oxazolidinone 20V, Positive-QTOFsplash10-000f-9000000000-7b0500ad1dd3ac06b3062021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Oxazolidinone 40V, Positive-QTOFsplash10-0006-9000000000-bbc7d76872c9e045ab862021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Oxazolidinone 10V, Negative-QTOFsplash10-000i-9000000000-1e250d4268f763330b032021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Oxazolidinone 20V, Negative-QTOFsplash10-0006-9000000000-f21c135752b102a3de342021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Oxazolidinone 40V, Negative-QTOFsplash10-0006-9000000000-fbe0411c4b16a9fc1c232021-10-12Wishart 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 IDNot Available
Chemspider ID66579
KEGG Compound IDC06695
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Oxazolidone
METLIN IDNot Available
PubChem Compound73949
PDB IDNot Available
ChEBI ID1237
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 ]