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Showing metabocard for (6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one (HMDB0257892)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 19:02:06 UTC
Update Date2021-09-26 23:14:30 UTC
HMDB IDHMDB0257892
Secondary Accession NumbersNone
Metabolite Identification
Common Name(6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one
Description5-thia-1-azabicyclo[4.2.0]oct-2-en-8-one belongs to the class of organic compounds known as cephems. These are organic compounds containing the 5-thia-1-azabicyclo[4.2.0]oct-2-en-8-one nucleus. Based on a literature review very few articles have been published on 5-thia-1-azabicyclo[4.2.0]oct-2-en-8-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). (6s)-5-thia-1-azabicyclo[4.2.0]oct-2-en-8-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one 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 HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)


  Mrv1652309112121022D          

  9 10  0  0  0  0            999 V2000
    3.1194    1.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1194    0.9760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4049    0.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6905    0.9760    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6905    1.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4049    2.2135    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8655    1.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8655    0.9760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2821    0.3926    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
Download

3D MOL for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)

HMDB0257892
     RDKit          3D
(6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one
 16 17  0  0  0  0  0  0  0  0999 V2000
   -2.9941    1.0129   -0.8218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0064    0.4190   -0.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7425   -0.5250    0.8234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6808   -1.0100   -0.1351 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8368   -1.5984    0.5988 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9374   -0.1835    0.6060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7670    0.7448   -0.5008 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5753    0.9741   -1.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6174    0.3604   -0.5832 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2941   -0.0361    1.6883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5769   -1.2184    1.0087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1288   -1.7216   -0.8584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9984   -0.5026    0.6673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7557    0.3635    1.5790 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6348    1.2411   -0.8858 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5357    1.6799   -1.8475 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  7  1  0
  7  8  2  0
  8  9  1  0
  9  2  1  0
  9  4  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
M  END
Download

3D SDF for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)


  Mrv1652309112121022D          

  9 10  0  0  0  0            999 V2000
    3.1194    1.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1194    0.9760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4049    0.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6905    0.9760    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6905    1.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4049    2.2135    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8655    1.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8655    0.9760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2821    0.3926    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257892

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CC2SCC=CN12

> <INCHI_IDENTIFIER>
InChI=1S/C6H7NOS/c8-5-4-6-7(5)2-1-3-9-6/h1-2,6H,3-4H2

> <INCHI_KEY>
FZEVMBJWXHDLDB-UHFFFAOYSA-N

> <FORMULA>
C6H7NOS

> <MOLECULAR_WEIGHT>
141.19

> <EXACT_MASS>
141.024835023

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
13.98563704869409

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-thia-1-azabicyclo[4.2.0]oct-2-en-8-one

> <ALOGPS_LOGP>
0.21

> <JCHEM_LOGP>
0.3706366773333334

> <ALOGPS_LOGS>
-0.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.292391491472337

> <JCHEM_PKA_STRONGEST_BASIC>
-7.064666809257221

> <JCHEM_POLAR_SURFACE_AREA>
20.310000000000002

> <JCHEM_REFRACTIVITY>
37.229200000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.80e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cephem

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)

HMDB0257892
     RDKit          3D
(6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one
 16 17  0  0  0  0  0  0  0  0999 V2000
   -2.9941    1.0129   -0.8218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0064    0.4190   -0.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7425   -0.5250    0.8234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6808   -1.0100   -0.1351 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8368   -1.5984    0.5988 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9374   -0.1835    0.6060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7670    0.7448   -0.5008 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5753    0.9741   -1.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6174    0.3604   -0.5832 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2941   -0.0361    1.6883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5769   -1.2184    1.0087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1288   -1.7216   -0.8584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9984   -0.5026    0.6673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7557    0.3635    1.5790 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6348    1.2411   -0.8858 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5357    1.6799   -1.8475 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  7  1  0
  7  8  2  0
  8  9  1  0
  9  2  1  0
  9  4  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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PDB for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)

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       5.823   3.362   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.823   1.822   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.489   1.052   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       3.156   1.822   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       3.156   3.362   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       4.489   4.132   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0       1.616   3.362   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.616   1.822   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.527   0.733   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    4    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
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3D PDB for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)

COMPND    HMDB0257892
HETATM    1  O1  UNL     1      -2.994   1.013  -0.822  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.006   0.419  -0.312  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.742  -0.525   0.823  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.681  -1.010  -0.135  1.00  0.00           C  
HETATM    5  S1  UNL     1       0.837  -1.598   0.599  1.00  0.00           S  
HETATM    6  C4  UNL     1       1.937  -0.183   0.606  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.767   0.745  -0.501  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.575   0.974  -1.027  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.617   0.360  -0.583  1.00  0.00           N  
HETATM   10  H1  UNL     1      -1.294  -0.036   1.688  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.577  -1.218   1.009  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.129  -1.722  -0.858  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.998  -0.503   0.667  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.756   0.363   1.579  1.00  0.00           H  
HETATM   15  H6  UNL     1       2.635   1.241  -0.886  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.536   1.680  -1.848  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4   10   11
CONECT    4    5    9   12
CONECT    5    6
CONECT    6    7   13   14
CONECT    7    8    8   15
CONECT    8    9   16
END
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SMILES for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)

O=C1CC2SCC=CN12
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INCHI for HMDB0257892 ((6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one)

InChI=1S/C6H7NOS/c8-5-4-6-7(5)2-1-3-9-6/h1-2,6H,3-4H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H7NOS
Average Molecular Weight141.19
Monoisotopic Molecular Weight141.024835023
IUPAC Name5-thia-1-azabicyclo[4.2.0]oct-2-en-8-one
Traditional Namecephem
CAS Registry NumberNot Available
SMILES
O=C1CC2SCC=CN12
InChI Identifier
InChI=1S/C6H7NOS/c8-5-4-6-7(5)2-1-3-9-6/h1-2,6H,3-4H2
InChI KeyFZEVMBJWXHDLDB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cephems. These are organic compounds containing the 5-thia-1-azabicyclo[4.2.0]Oct-2-en-8-one nucleus.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactams
Sub ClassBeta lactams
Direct ParentCephems
Alternative Parents
Substituents
  • Cephem
  • Meta-thiazine
  • Tertiary carboxylic acid amide
  • Azetidine
  • Carboxamide group
  • Dialkylthioether
  • Hemithioaminal
  • Thioether
  • Carboxylic acid derivative
  • Azacycle
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
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
logP0.21ALOGPS
logP0.37ChemAxon
logS-0.39ALOGPS
pKa (Strongest Acidic)19.29ChemAxon
pKa (Strongest Basic)-7.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area20.31 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.23 m³·mol⁻¹ChemAxon
Polarizability13.99 ųChemAxon
Number of Rings2ChemAxon
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-2H]-161.56230932474
DeepCCS[M+Na]+136.29830932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-oneO=C1CC2SCC=CN122250.1Standard polar33892256
(6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-oneO=C1CC2SCC=CN121236.6Standard non polar33892256
(6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-oneO=C1CC2SCC=CN121381.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - (6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one GC-MS (Non-derivatized) - 70eV, Positivesplash10-002f-9200000000-5301f7eab6ebc420c71d2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (6S)-5-Thia-1-azabicyclo[4.2.0]oct-2-en-8-one GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart 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 ID10655149
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound18179538
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. 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 ]