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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
Description2-Oxazolidinone 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. 2-Oxazolidinone 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 a significant number of articles have been published on 2-Oxazolidinone. 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 oneHMDB
1,3 Oxazolidine 2 oneHMDB
1,3-Oxazolidin-2-oneHMDB
1,3-Oxazolidine-2-oneHMDB
2 OxazolidoneHMDB
2 OxazolidinoneHMDB
2-OxazolidoneHMDB
Oxazolidin 2 oneHMDB
OxazolidinoneHMDB
OxazolidinonesHMDB
Oxazolidin-2-oneHMDB
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 locationSource
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
Predicted Chromatographic Properties
Spectra
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 ]