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Showing metabocard for Carbapenem (HMDB0249611)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 04:07:39 UTC
Update Date2021-09-26 23:00:36 UTC
HMDB IDHMDB0249611
Secondary Accession NumbersNone
Metabolite Identification
Common NameCarbapenem
Description1-azabicyclo[3.2.0]hept-2-en-7-one belongs to the class of organic compounds known as carbapenems. These are beta-lactam derivatives in which the beta-lactam ring shares the nitrogen atom with a pyrrole-2-carboxylic acid. Based on a literature review very few articles have been published on 1-azabicyclo[3.2.0]hept-2-en-7-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Carbapenem is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Carbapenem 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 HMDB0249611 (Carbapenem)


  Mrv1652309112106072D          

  8  9  0  0  0  0            999 V2000
    2.5579    1.6561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428    0.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.3212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    0.5762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    1.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    1.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.5762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -0.0072    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
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
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3D MOL for HMDB0249611 (Carbapenem)

HMDB0249611
     RDKit          3D
Carbapenem
 15 16  0  0  0  0  0  0  0  0999 V2000
   -2.6296    0.9979   -1.4075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6701    0.5984   -0.7015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5497   -0.2056    0.5716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133   -0.7039   -0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9691   -0.7107    0.7068 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8425    0.2755   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0859    1.0420   -0.7876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2668    0.6528   -0.6721 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3281    0.5060    1.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3658   -0.9083    0.7401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4201   -1.5079   -0.8094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8474   -0.4995    1.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4280   -1.7124    0.5851 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8992    0.3397    0.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4713    1.8363   -1.4109 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
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0249611 (Carbapenem)


  Mrv1652309112106072D          

  8  9  0  0  0  0            999 V2000
    2.5579    1.6561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428    0.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.3212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    0.5762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    1.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    1.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.5762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -0.0072    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
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249611

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CC2CC=CN12

> <INCHI_IDENTIFIER>
InChI=1S/C6H7NO/c8-6-4-5-2-1-3-7(5)6/h1,3,5H,2,4H2

> <INCHI_KEY>
YZBQHRLRFGPBSL-UHFFFAOYSA-N

> <FORMULA>
C6H7NO

> <MOLECULAR_WEIGHT>
109.128

> <EXACT_MASS>
109.052763849

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.162948014069837

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.09

> <JCHEM_LOGP>
-0.1670508560000003

> <ALOGPS_LOGS>
0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.335923982189209

> <JCHEM_POLAR_SURFACE_AREA>
20.310000000000002

> <JCHEM_REFRACTIVITY>
29.7039

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.24e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
carbapenem RS 533

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0249611 (Carbapenem)

HMDB0249611
     RDKit          3D
Carbapenem
 15 16  0  0  0  0  0  0  0  0999 V2000
   -2.6296    0.9979   -1.4075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6701    0.5984   -0.7015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5497   -0.2056    0.5716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133   -0.7039   -0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9691   -0.7107    0.7068 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8425    0.2755   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0859    1.0420   -0.7876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2668    0.6528   -0.6721 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3281    0.5060    1.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3658   -0.9083    0.7401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4201   -1.5079   -0.8094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8474   -0.4995    1.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4280   -1.7124    0.5851 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8992    0.3397    0.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4713    1.8363   -1.4109 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
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0249611 (Carbapenem)

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       4.775   3.091   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.680   1.846   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.775   0.600   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       3.310   1.076   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       3.310   2.616   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.770   2.616   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.770   1.076   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.681  -0.013   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    4    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   18    0
END
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3D PDB for HMDB0249611 (Carbapenem)

COMPND    HMDB0249611
HETATM    1  O1  UNL     1      -2.630   0.998  -1.408  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.670   0.598  -0.701  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.550  -0.206   0.572  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.313  -0.704  -0.087  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.969  -0.711   0.707  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.843   0.275  -0.002  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.086   1.042  -0.788  1.00  0.00           C  
HETATM    8  N1  UNL     1      -0.267   0.653  -0.672  1.00  0.00           N  
HETATM    9  H1  UNL     1      -1.328   0.506   1.394  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.366  -0.908   0.740  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.420  -1.508  -0.809  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.847  -0.500   1.766  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.428  -1.712   0.585  1.00  0.00           H  
HETATM   14  H6  UNL     1       2.899   0.340   0.115  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.471   1.836  -1.411  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   12   13
CONECT    6    7    7   14
CONECT    7    8   15
END
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SMILES for HMDB0249611 (Carbapenem)

O=C1CC2CC=CN12
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INCHI for HMDB0249611 (Carbapenem)

InChI=1S/C6H7NO/c8-6-4-5-2-1-3-7(5)6/h1,3,5H,2,4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H7NO
Average Molecular Weight109.128
Monoisotopic Molecular Weight109.052763849
IUPAC Name1-azabicyclo[3.2.0]hept-2-en-7-one
Traditional Namecarbapenem RS 533
CAS Registry NumberNot Available
SMILES
O=C1CC2CC=CN12
InChI Identifier
InChI=1S/C6H7NO/c8-6-4-5-2-1-3-7(5)6/h1,3,5H,2,4H2
InChI KeyYZBQHRLRFGPBSL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carbapenems. These are beta-lactam derivatives in which the beta-lactam ring shares the nitrogen atom with a pyrrole-2-carboxylic acid.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactams
Sub ClassBeta lactams
Direct ParentCarbapenems
Alternative Parents
Substituents
  • Carbapenem
  • Azepine
  • Tertiary carboxylic acid amide
  • Pyrroline
  • Azetidine
  • Carboxamide group
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • 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
logP0.09ALOGPS
logP-0.17ChemAxon
logS0.76ALOGPS
pKa (Strongest Basic)-6.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area20.31 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.7 m³·mol⁻¹ChemAxon
Polarizability11.16 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]-156.55130932474
DeepCCS[M+Na]+131.16930932474
AllCCS[M+H]+122.432859911
AllCCS[M+H-H2O]+117.432859911
AllCCS[M+NH4]+127.132859911
AllCCS[M+Na]+128.532859911
AllCCS[M-H]-119.732859911
AllCCS[M+Na-2H]-121.632859911
AllCCS[M+HCOO]-123.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CarbapenemO=C1CC2CC=CN121710.4Standard polar33892256
CarbapenemO=C1CC2CC=CN121060.6Standard non polar33892256
CarbapenemO=C1CC2CC=CN121111.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Carbapenem GC-MS (Non-derivatized) - 70eV, Positivesplash10-00ou-9000000000-e7a6c39157cf3e8df6362021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Carbapenem 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 - Carbapenem 10V, Positive-QTOFsplash10-03di-0900000000-c89e2460dc3caf4abe052021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Carbapenem 20V, Positive-QTOFsplash10-03e9-9800000000-c2e0500821561c9b585e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Carbapenem 40V, Positive-QTOFsplash10-0f8c-9000000000-67c2f9752d7e6ab0d0972021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Carbapenem 10V, Negative-QTOFsplash10-0a4i-1900000000-4c33d7611b8fc11c3d1f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Carbapenem 20V, Negative-QTOFsplash10-0aor-8900000000-fb8055de9bff34bf69432021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Carbapenem 40V, Negative-QTOFsplash10-001i-9000000000-d580ab77159bc87bee052021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID14242788
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13293130
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 ]