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Showing metabocard for Succinimide (HMDB0240653)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2020-06-03 19:55:51 UTC
Update Date2022-09-22 18:34:32 UTC
HMDB IDHMDB0240653
Secondary Accession NumbersNone
Metabolite Identification
Common NameSuccinimide
Descriptionsuccinimide, also known as butanimide, belongs to the class of organic compounds known as pyrrolidine-2-ones. These are pyrrolidines which bear a C=O group at position 2 of the pyrrolidine ring. Based on a literature review a significant number of articles have been published on succinimide.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0240653 (Succinimide)

  Mrv1652306042020222D          

  7  7  0  0  0  0            999 V2000
   -1.3727    1.4718    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0401    0.9868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7852    0.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9602    0.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7053    0.9868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8247    1.2417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0792    1.2417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  2  0  0  0  0
  2  6  2  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
M  END
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3D MOL for HMDB0240653 (Succinimide)

HMDB0240653
     RDKit          3D
Succinimide
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.3572   -0.7783   -0.3608 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2521   -0.2886   -0.0734 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0376   -1.0932    0.3114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0599   -0.2066   -0.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5825    1.1461    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2461    2.1535    0.4684 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8340    1.0841   -0.0258 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0480   -2.0939   -0.1252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1072   -1.0684    1.4031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0480   -0.4551    0.0861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0085   -0.2657   -1.4127 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5234    1.8662   -0.0811 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  2  0
  5  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  7 12  1  0
M  END
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3D SDF for HMDB0240653 (Succinimide)

  Mrv1652306042020222D          

  7  7  0  0  0  0            999 V2000
   -1.3727    1.4718    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0401    0.9868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7852    0.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9602    0.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7053    0.9868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8247    1.2417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0792    1.2417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  2  0  0  0  0
  2  6  2  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0240653

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7)

> <INCHI_KEY>
KZNICNPSHKQLFF-UHFFFAOYSA-N

> <FORMULA>
C4H5NO2

> <MOLECULAR_WEIGHT>
99.089

> <EXACT_MASS>
99.032028405

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.819566635394999

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrrolidine-2,5-dione

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.993471561

> <ALOGPS_LOGS>
0.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.896563297180688

> <JCHEM_PKA_STRONGEST_BASIC>
-7.226714232018063

> <JCHEM_POLAR_SURFACE_AREA>
46.17

> <JCHEM_REFRACTIVITY>
22.2814

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.28e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
succinimide

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0240653 (Succinimide)

HMDB0240653
     RDKit          3D
Succinimide
 12 12  0  0  0  0  0  0  0  0999 V2000
    2.3572   -0.7783   -0.3608 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2521   -0.2886   -0.0734 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0376   -1.0932    0.3114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0599   -0.2066   -0.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5825    1.1461    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2461    2.1535    0.4684 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8340    1.0841   -0.0258 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0480   -2.0939   -0.1252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1072   -1.0684    1.4031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0480   -0.4551    0.0861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0085   -0.2657   -1.4127 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5234    1.8662   -0.0811 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  2  0
  5  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  7 12  1  0
M  END
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PDB for HMDB0240653 (Succinimide)

HEADER    PROTEIN                                 04-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-20         0                                  
HETATM    1  N   UNK     0      -2.562   2.747   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -3.808   1.842   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.332   0.377   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.792   0.377   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.317   1.842   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -5.273   2.318   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.148   2.318   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    3    6    1                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    7    1                                                  
CONECT    6    2                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0240653 (Succinimide)

COMPND    HMDB0240653
HETATM    1  O1  UNL     1       2.357  -0.778  -0.361  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.252  -0.289  -0.073  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.038  -1.093   0.311  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.060  -0.207  -0.290  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.583   1.146   0.100  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.246   2.153   0.468  1.00  0.00           O  
HETATM    7  N1  UNL     1       0.834   1.084  -0.026  1.00  0.00           N  
HETATM    8  H1  UNL     1       0.048  -2.094  -0.125  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.107  -1.068   1.403  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.048  -0.455   0.086  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.009  -0.266  -1.413  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.523   1.866  -0.081  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5   10   11
CONECT    5    6    6    7
CONECT    7   12
END
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SMILES for HMDB0240653 (Succinimide)

O=C1CCC(=O)N1
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INCHI for HMDB0240653 (Succinimide)

InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,5-DiketopyrrolidineChEBI
2,5-DioxopyrrolidineChEBI
2,5-PyrrolidinedioneChEBI
3,4-Dihydropyrrole-2,5-dioneChEBI
ButanimideChEBI
Dihydro-3-pyrroline-2,5-dioneChEBI
Succinic acid imideChEBI
Succinic imideChEBI
Succinimide pharbiolKegg
Succinate imideGenerator
SuccinimideHMDB
Chemical FormulaC4H5NO2
Average Molecular Weight99.089
Monoisotopic Molecular Weight99.032028405
IUPAC Namepyrrolidine-2,5-dione
Traditional Namesuccinimide
CAS Registry Number123-56-8
SMILES
O=C1CCC(=O)N1
InChI Identifier
InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7)
InChI KeyKZNICNPSHKQLFF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidine-2-ones. These are pyrrolidines which bear a C=O group at position 2 of the pyrrolidine ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolidines
Sub ClassPyrrolidones
Direct ParentPyrrolidine-2-ones
Alternative Parents
Substituents
  • 2-pyrrolidone
  • Carboxylic acid imide
  • Dicarboximide
  • Carboxylic acid imide, n-unsubstituted
  • Lactam
  • Carboxylic acid derivative
  • Azacycle
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10955
KEGG Compound IDC07273
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSuccinimide
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID9307
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1284781
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Zhang T, Creek DJ, Barrett MP, Blackburn G, Watson DG: Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine. Anal Chem. 2012 Feb 21;84(4):1994-2001. doi: 10.1021/ac2030738. Epub 2012 Feb 1. [PubMed:22409530 ]