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Showing metabocard for Penem (HMDB0256222)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:32:51 UTC
Update Date2021-09-26 23:11:43 UTC
HMDB IDHMDB0256222
Secondary Accession NumbersNone
Metabolite Identification
Common NamePenem
DescriptionPenem belongs to the class of organic compounds known as penems. These are organic heterocyclic compounds containing a penem moiety, which is a 2,3-didehydropenam derivative. Based on a literature review a significant number of articles have been published on Penem. This compound has been identified in human blood as reported by (PMID: 31557052 ). Penem is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Penem 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 HMDB0256222 (Penem)

  Mrv1652309112118332D          

  8  9  0  0  0  0            999 V2000
   -0.1477   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773   -0.1073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477   -0.1073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7310    0.4761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620   -1.1872    0.0000 S   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
  1  4  1  0  0  0  0
  4  5  2  0  0  0  0
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
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3D MOL for HMDB0256222 (Penem)

HMDB0256222
     RDKit          3D
Penem
 13 14  0  0  0  0  0  0  0  0999 V2000
   -2.0249   -0.4940    1.8630 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3369   -0.2425    0.8714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6594    0.1258   -0.5357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2851    0.6954   -0.4936 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9191   -0.0673   -1.6774 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1394   -0.3759   -0.3998 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4757   -0.3988    0.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0836   -0.1931    0.6325 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8584   -0.6940   -1.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4117    0.9630   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1411    1.7536   -0.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1751   -0.5064   -0.5703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9248   -0.5658    1.7326 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  2  0
  7  8  1  0
  8  2  1  0
  8  4  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  6 12  1  0
  7 13  1  0
M  END
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3D SDF for HMDB0256222 (Penem)

  Mrv1652309112118332D          

  8  9  0  0  0  0            999 V2000
   -0.1477   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773   -0.1073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477   -0.1073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7310    0.4761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620   -1.1872    0.0000 S   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
  1  4  1  0  0  0  0
  4  5  2  0  0  0  0
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256222

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CC2SC=CN12

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NOS/c7-4-3-5-6(4)1-2-8-5/h1-2,5H,3H2

> <INCHI_KEY>
HHXMXAQDOUCLDN-UHFFFAOYSA-N

> <FORMULA>
C5H5NOS

> <MOLECULAR_WEIGHT>
127.16

> <EXACT_MASS>
127.009184959

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
11.983736696894699

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-thia-1-azabicyclo[3.2.0]hept-2-en-7-one

> <ALOGPS_LOGP>
-0.31

> <JCHEM_LOGP>
-0.14019963766666682

> <ALOGPS_LOGS>
-0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.12582981653831

> <JCHEM_PKA_STRONGEST_BASIC>
-7.593365591925965

> <JCHEM_POLAR_SURFACE_AREA>
20.310000000000002

> <JCHEM_REFRACTIVITY>
31.950499999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-thia-1-azabicyclo[3.2.0]hept-2-en-7-one

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0256222 (Penem)

HMDB0256222
     RDKit          3D
Penem
 13 14  0  0  0  0  0  0  0  0999 V2000
   -2.0249   -0.4940    1.8630 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3369   -0.2425    0.8714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6594    0.1258   -0.5357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2851    0.6954   -0.4936 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9191   -0.0673   -1.6774 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1394   -0.3759   -0.3998 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4757   -0.3988    0.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0836   -0.1931    0.6325 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8584   -0.6940   -1.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4117    0.9630   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1411    1.7536   -0.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1751   -0.5064   -0.5703 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9248   -0.5658    1.7326 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  2  0
  7  8  1  0
  8  2  1  0
  8  4  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  6 12  1  0
  7 13  1  0
M  END
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PDB for HMDB0256222 (Penem)

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      -0.276  -1.740   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.264  -1.740   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.264  -0.200   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -0.276  -0.200   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.365   0.889   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.729   0.276   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.634  -0.970   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0       2.729  -2.216   0.000  0.00  0.00           S+0
CONECT    1    2    4                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    1    5                                                  
CONECT    5    4                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   18    0
END
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3D PDB for HMDB0256222 (Penem)

COMPND    HMDB0256222
HETATM    1  O1  UNL     1      -2.025  -0.494   1.863  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.337  -0.243   0.871  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.659   0.126  -0.536  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.285   0.695  -0.494  1.00  0.00           C  
HETATM    5  S1  UNL     1       0.919  -0.067  -1.677  1.00  0.00           S  
HETATM    6  C4  UNL     1       2.139  -0.376  -0.400  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.476  -0.399   0.726  1.00  0.00           C  
HETATM    8  N1  UNL     1       0.084  -0.193   0.633  1.00  0.00           N  
HETATM    9  H1  UNL     1      -1.858  -0.694  -1.219  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.412   0.963  -0.612  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.141   1.754  -0.318  1.00  0.00           H  
HETATM   12  H4  UNL     1       3.175  -0.506  -0.570  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.925  -0.566   1.733  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    9   10
CONECT    4    5    8   11
CONECT    5    6
CONECT    6    7    7   12
CONECT    7    8   13
END
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SMILES for HMDB0256222 (Penem)

O=C1CC2SC=CN12
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INCHI for HMDB0256222 (Penem)

InChI=1S/C5H5NOS/c7-4-3-5-6(4)1-2-8-5/h1-2,5H,3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H5NOS
Average Molecular Weight127.16
Monoisotopic Molecular Weight127.009184959
IUPAC Name4-thia-1-azabicyclo[3.2.0]hept-2-en-7-one
Traditional Name4-thia-1-azabicyclo[3.2.0]hept-2-en-7-one
CAS Registry NumberNot Available
SMILES
O=C1CC2SC=CN12
InChI Identifier
InChI=1S/C5H5NOS/c7-4-3-5-6(4)1-2-8-5/h1-2,5H,3H2
InChI KeyHHXMXAQDOUCLDN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as penems. These are organic heterocyclic compounds containing a penem moiety, which is a 2,3-didehydropenam derivative.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactams
Sub ClassBeta lactams
Direct ParentPenems
Alternative Parents
Substituents
  • Penem
  • Tertiary carboxylic acid amide
  • Meta-thiazoline
  • Azetidine
  • Carboxamide group
  • Thioenolether
  • Carboxylic acid derivative
  • Azacycle
  • Hemithioaminal
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
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

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-158.51630932474
DeepCCS[M+Na]+133.15730932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PenemO=C1CC2SC=CN121969.3Standard polar33892256
PenemO=C1CC2SC=CN121162.5Standard non polar33892256
PenemO=C1CC2SC=CN121273.0Semi standard non polar33892256
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 ID14503135
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPenem
METLIN IDNot Available
PubChem Compound19980826
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 ]