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Showing metabocard for Glycidamide (HMDB0252860)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 10:57:20 UTC
Update Date2021-09-26 23:05:44 UTC
HMDB IDHMDB0252860
Secondary Accession NumbersNone
Metabolite Identification
Common NameGlycidamide
Descriptionoxirane-2-carboximidic acid belongs to the class of organic compounds known as oxirane carboxylic acids and derivatives. Oxirane carboxylic acids and derivatives are compounds containing an oxirane ring bearing a carboxylic acid group (or a derivative thereof). oxirane-2-carboximidic acid is a very strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Glycidamide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Glycidamide 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 HMDB0252860 (Glycidamide)


  Mrv1572004221603512D          

  6  6  0  0  0  0            999 V2000
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
M  END
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3D MOL for HMDB0252860 (Glycidamide)

HMDB0252860
     RDKit          3D
Glycidamide
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.5246    0.9806   -0.8037 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8824    0.0189   -0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3388   -1.2721   -0.5000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2888    0.3111    0.5800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5774   -0.3244    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9475   -0.7158    1.2358 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107    1.9490   -0.6445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2361   -1.5238   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3328    1.3262    1.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391   -1.0336   -0.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5070    0.2838    0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  4  1  0
  1  7  1  0
  3  8  1  0
  4  9  1  0
  5 10  1  0
  5 11  1  0
M  END
Download

3D SDF for HMDB0252860 (Glycidamide)


  Mrv1572004221603512D          

  6  6  0  0  0  0            999 V2000
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252860

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=N)C1CO1

> <INCHI_IDENTIFIER>
InChI=1S/C3H5NO2/c4-3(5)2-1-6-2/h2H,1H2,(H2,4,5)

> <INCHI_KEY>
FMAZQSYXRGRESX-UHFFFAOYSA-N

> <FORMULA>
C3H5NO2

> <MOLECULAR_WEIGHT>
87.078

> <EXACT_MASS>
87.032028405

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
7.723803826215535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxirane-2-carboximidic acid

> <ALOGPS_LOGP>
-1.36

> <JCHEM_LOGP>
-2.989300679332414

> <ALOGPS_LOGS>
-0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.466403322834882

> <JCHEM_PKA_STRONGEST_BASIC>
12.54833187046645

> <JCHEM_POLAR_SURFACE_AREA>
53.31

> <JCHEM_REFRACTIVITY>
29.6322

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
oxirane-2-carboximidic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0252860 (Glycidamide)

HMDB0252860
     RDKit          3D
Glycidamide
 11 11  0  0  0  0  0  0  0  0999 V2000
    1.5246    0.9806   -0.8037 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8824    0.0189   -0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3388   -1.2721   -0.5000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2888    0.3111    0.5800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5774   -0.3244    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9475   -0.7158    1.2358 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107    1.9490   -0.6445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2361   -1.5238   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3328    1.3262    1.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391   -1.0336   -0.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5070    0.2838    0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  4  1  0
  1  7  1  0
  3  8  1  0
  4  9  1  0
  5 10  1  0
  5 11  1  0
M  END
Download

PDB for HMDB0252860 (Glycidamide)

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -0.889   3.969   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       1.778   3.969   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -0.325   0.325   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0252860 (Glycidamide)

COMPND    HMDB0252860
HETATM    1  N1  UNL     1       1.525   0.981  -0.804  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.882   0.019  -0.260  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.339  -1.272  -0.500  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.289   0.311   0.580  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.577  -0.324   0.069  1.00  0.00           C  
HETATM    6  O2  UNL     1      -0.947  -0.716   1.236  1.00  0.00           O  
HETATM    7  H1  UNL     1       1.211   1.949  -0.645  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.236  -1.524  -0.067  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.333   1.326   1.012  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.539  -1.034  -0.755  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.507   0.284   0.134  1.00  0.00           H  
CONECT    1    2    2    7
CONECT    2    3    4
CONECT    3    8
CONECT    4    5    6    9
CONECT    5    6   10   11
END
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SMILES for HMDB0252860 (Glycidamide)

OC(=N)C1CO1
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INCHI for HMDB0252860 (Glycidamide)

InChI=1S/C3H5NO2/c4-3(5)2-1-6-2/h2H,1H2,(H2,4,5)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Oxirane-2-carboximidateGenerator
GlycidamideMeSH
Oxirane-2-carboxamideMeSH
(+--)-OxiranecarboxamideMeSH
2,3-EpoxypropanamideMeSH
2-OxiranecarboxamideMeSH
Glycidic acid amideMeSH
OxiranecarboxamideMeSH
Chemical FormulaC3H5NO2
Average Molecular Weight87.078
Monoisotopic Molecular Weight87.032028405
IUPAC Nameoxirane-2-carboximidic acid
Traditional Nameoxirane-2-carboximidic acid
CAS Registry NumberNot Available
SMILES
OC(=N)C1CO1
InChI Identifier
InChI=1S/C3H5NO2/c4-3(5)2-1-6-2/h2H,1H2,(H2,4,5)
InChI KeyFMAZQSYXRGRESX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxirane carboxylic acids and derivatives. Oxirane carboxylic acids and derivatives are compounds containing an oxirane ring bearing a carboxylic acid group (or a derivative thereof).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassEpoxides
Sub ClassOxirane carboxylic acids and derivatives
Direct ParentOxirane carboxylic acids and derivatives
Alternative Parents
Substituents
  • Oxirane carboxylic acid or derivatives
  • Carboxamide group
  • Primary carboxylic acid amide
  • Carboxylic acid derivative
  • Dialkyl ether
  • Ether
  • Oxacycle
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP-1.4ALOGPS
logP-3ChemAxon
logS-0.89ALOGPS
pKa (Strongest Acidic)-3.5ChemAxon
pKa (Strongest Basic)12.55ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area53.31 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.63 m³·mol⁻¹ChemAxon
Polarizability7.72 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+122.72630932474
DeepCCS[M-H]-120.8330932474
DeepCCS[M-2H]-156.43430932474
DeepCCS[M+Na]+130.92830932474
AllCCS[M+H]+120.532859911
AllCCS[M+H-H2O]+115.632859911
AllCCS[M+NH4]+125.132859911
AllCCS[M+Na]+126.432859911
AllCCS[M-H]-115.732859911
AllCCS[M+Na-2H]-119.432859911
AllCCS[M+HCOO]-123.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
GlycidamideOC(=N)C1CO11932.1Standard polar33892256
GlycidamideOC(=N)C1CO11008.1Standard non polar33892256
GlycidamideOC(=N)C1CO11211.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Glycidamide,2TMS,isomer #1C[Si](C)(C)N=C(O[Si](C)(C)C)C1CO11143.4Semi standard non polar33892256
Glycidamide,2TMS,isomer #1C[Si](C)(C)N=C(O[Si](C)(C)C)C1CO11108.7Standard non polar33892256
Glycidamide,2TMS,isomer #1C[Si](C)(C)N=C(O[Si](C)(C)C)C1CO11378.2Standard polar33892256
Glycidamide,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N=C(O[Si](C)(C)C(C)(C)C)C1CO11543.6Semi standard non polar33892256
Glycidamide,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N=C(O[Si](C)(C)C(C)(C)C)C1CO11486.7Standard non polar33892256
Glycidamide,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N=C(O[Si](C)(C)C(C)(C)C)C1CO11618.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Glycidamide GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-4f88fb2718509483fc8d2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidamide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidamide GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidamide GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidamide GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Glycidamide GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 10V, Positive-QTOFsplash10-0079-9000000000-b5cc9602d064be7334972016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 20V, Positive-QTOFsplash10-00di-9000000000-ba1d9f966bcc79b82d332016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 40V, Positive-QTOFsplash10-006y-9000000000-9f0db03e0299a5a90f602016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 10V, Negative-QTOFsplash10-000i-9000000000-2801b03de8f97309ed622016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 20V, Negative-QTOFsplash10-00ku-9000000000-470d9efc569c13d3df582016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 40V, Negative-QTOFsplash10-0006-9000000000-e989a8c8740c8f00b1082016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 10V, Positive-QTOFsplash10-0076-9000000000-10c2712d263aed4ec5382021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 20V, Positive-QTOFsplash10-0006-9000000000-5f8f29713031c31020d52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 40V, Positive-QTOFsplash10-0udl-9000000000-c987d1d6ad804849e4802021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 10V, Negative-QTOFsplash10-000i-9000000000-22244befa4ac0b615fad2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 20V, Negative-QTOFsplash10-052f-9000000000-856ba165b528c63c678f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glycidamide 40V, Negative-QTOFsplash10-0006-9000000000-20b0928d2d4f9efebdba2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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 NMR1H NMR Spectrum (1D, 1000 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, 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 NMR1H NMR Spectrum (1D, 400 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, 500 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 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 NMR13C NMR Spectrum (1D, 700 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, 800 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, 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound91550
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 ]