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Showing metabocard for N-Methylsuccinimide (HMDB0255192)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 14:46:13 UTC
Update Date2021-09-26 23:09:48 UTC
HMDB IDHMDB0255192
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-Methylsuccinimide
DescriptionN-Methylsuccinimide belongs to the class of organic compounds known as n-substituted carboxylic acid imides. N-substituted carboxylic acid imides are compounds comprising an N-substituted carboxylic acid imide group, with the general structure R1N(C(R2)=O)C(R3)=O (R2,R3=H, alkyl, aryl; R1=Anything but H). N-Methylsuccinimide is an extremely weak basic (essentially neutral) compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). N-methylsuccinimide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-Methylsuccinimide 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 HMDB0255192 (N-Methylsuccinimide)


  Mrv0541 05041406492D          

  8  8  0  0  0  0            999 V2000
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    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
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   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
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  2  0  0  0  0
M  END
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3D MOL for HMDB0255192 (N-Methylsuccinimide)

HMDB0255192
     RDKit          3D
N-Methylsuccinimide
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1390    0.0535   -0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6889    0.0043   -0.0221 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1167    1.0790    0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2868    2.2459    0.6469 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4677    0.4976    0.6325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4983   -0.5061   -0.5077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1534   -1.1147   -0.3325 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2267   -2.3066   -0.4194 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5243   -0.9426   -0.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4440    0.7467   -0.9659 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6331    0.3143    0.8100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2778    1.2411    0.5634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5269   -0.1095    1.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3058   -1.2526   -0.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5963    0.0497   -1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
M  END
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3D SDF for HMDB0255192 (N-Methylsuccinimide)


  Mrv0541 05041406492D          

  8  8  0  0  0  0            999 V2000
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    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
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   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
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255192

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)CCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c1-6-4(7)2-3-5(6)8/h2-3H2,1H3

> <INCHI_KEY>
KYEACNNYFNZCST-UHFFFAOYSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.1146

> <EXACT_MASS>
113.047678473

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
10.823060981799907

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methylpyrrolidine-2,5-dione

> <ALOGPS_LOGP>
-0.70

> <JCHEM_LOGP>
-0.7697954953333332

> <ALOGPS_LOGS>
0.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.9365357276743

> <JCHEM_POLAR_SURFACE_AREA>
37.38

> <JCHEM_REFRACTIVITY>
27.1781

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-methylsuccinimide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0255192 (N-Methylsuccinimide)

HMDB0255192
     RDKit          3D
N-Methylsuccinimide
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1390    0.0535   -0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6889    0.0043   -0.0221 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1167    1.0790    0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2868    2.2459    0.6469 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4677    0.4976    0.6325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4983   -0.5061   -0.5077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1534   -1.1147   -0.3325 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2267   -2.3066   -0.4194 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5243   -0.9426   -0.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4440    0.7467   -0.9659 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6331    0.3143    0.8100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2778    1.2411    0.5634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5269   -0.1095    1.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3058   -1.2526   -0.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5963    0.0497   -1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
M  END
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PDB for HMDB0255192 (N-Methylsuccinimide)

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    6    8                                                  
CONECT    6    1    4    5                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0255192 (N-Methylsuccinimide)

COMPND    HMDB0255192
HETATM    1  C1  UNL     1       2.139   0.053  -0.160  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.689   0.004  -0.022  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.117   1.079   0.449  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.287   2.246   0.647  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.468   0.498   0.632  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.498  -0.506  -0.508  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.153  -1.115  -0.333  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.227  -2.307  -0.419  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.524  -0.943  -0.435  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.444   0.747  -0.966  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.633   0.314   0.810  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.278   1.241   0.563  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.527  -0.109   1.566  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.306  -1.253  -0.365  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.596   0.050  -1.460  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    7
CONECT    3    4    4    5
CONECT    5    6   12   13
CONECT    6    7   14   15
CONECT    7    8    8
END
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SMILES for HMDB0255192 (N-Methylsuccinimide)

CN1C(=O)CCC1=O
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INCHI for HMDB0255192 (N-Methylsuccinimide)

InChI=1S/C5H7NO2/c1-6-4(7)2-3-5(6)8/h2-3H2,1H3
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Synonyms
ValueSource
MSIMeSH
Chemical FormulaC5H7NO2
Average Molecular Weight113.1146
Monoisotopic Molecular Weight113.047678473
IUPAC Name1-methylpyrrolidine-2,5-dione
Traditional NameN-methylsuccinimide
CAS Registry NumberNot Available
SMILES
CN1C(=O)CCC1=O
InChI Identifier
InChI=1S/C5H7NO2/c1-6-4(7)2-3-5(6)8/h2-3H2,1H3
InChI KeyKYEACNNYFNZCST-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-substituted carboxylic acid imides. N-substituted carboxylic acid imides are compounds comprising an N-substituted carboxylic acid imide group, with the general structure R1N(C(R2)=O)C(R3)=O (R2,R3=H, alkyl, aryl; R1=Anything but H).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acid derivatives
Direct ParentN-substituted carboxylic acid imides
Alternative Parents
Substituents
  • Carboxylic acid imide, n-substituted
  • Pyrrolidone
  • 2-pyrrolidone
  • N-alkylpyrrolidine
  • Dicarboximide
  • Pyrrolidine
  • Lactam
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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-0.7ALOGPS
logP-0.77ChemAxon
logS0.8ALOGPS
pKa (Strongest Basic)-6.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area37.38 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.18 m³·mol⁻¹ChemAxon
Polarizability10.82 ųChemAxon
Number of Rings1ChemAxon
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+H]+120.86530932474
DeepCCS[M-H]-118.35430932474
DeepCCS[M-2H]-154.54430932474
DeepCCS[M+Na]+129.24430932474
AllCCS[M+H]+123.932859911
AllCCS[M+H-H2O]+119.132859911
AllCCS[M+NH4]+128.432859911
AllCCS[M+Na]+129.732859911
AllCCS[M-H]-120.832859911
AllCCS[M+Na-2H]-123.432859911
AllCCS[M+HCOO]-126.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-MethylsuccinimideCN1C(=O)CCC1=O1813.2Standard polar33892256
N-MethylsuccinimideCN1C(=O)CCC1=O1105.2Standard non polar33892256
N-MethylsuccinimideCN1C(=O)CCC1=O1094.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N-Methylsuccinimide GC-MS (Non-derivatized) - 70eV, Positivesplash10-0bvl-9100000000-695d4a802439535dc3f32021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Methylsuccinimide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart 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 Compound70717
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 ]