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Showing metabocard for 3-Hydroxy-1-methylpyrrolidine-2,5-dione (HMDB0245148)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:14:54 UTC
Update Date2021-09-26 22:53:26 UTC
HMDB IDHMDB0245148
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Hydroxy-1-methylpyrrolidine-2,5-dione
Description3-Hydroxy-1-methylpyrrolidine-2,5-dione, also known as 2-HMSI or 2-hydroxy-N-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). Based on a literature review a significant number of articles have been published on 3-Hydroxy-1-methylpyrrolidine-2,5-dione. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-hydroxy-1-methylpyrrolidine-2,5-dione is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Hydroxy-1-methylpyrrolidine-2,5-dione 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 HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

  Mrv1652309112100152D          

  9  9  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   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
    2.0198    0.8843    0.0000 O   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
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  6  9  1  0  0  0  0
M  END
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3D MOL for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

HMDB0245148
     RDKit          3D
3-Hydroxy-1-methylpyrrolidine-2,5-dione
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.1775    0.0323    0.0511 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7302    0.1216   -0.0682 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1190    0.9490    0.7140 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1749    1.6575    1.7056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4813    0.8330    0.1374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4464   -0.5771   -0.4142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4347   -1.4379    0.6908 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0877   -0.6166   -1.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -1.1213   -2.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6442    0.6554   -0.7497 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5426   -1.0036   -0.1333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5129    0.3190    1.0563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2773    1.0063    0.8569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5344    1.5152   -0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2425   -0.7882   -1.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5240   -1.5447    1.0652 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
  6  8  1  0
  8  9  2  0
  8  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
M  END
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3D SDF for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

  Mrv1652309112100152D          

  9  9  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   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
    2.0198    0.8843    0.0000 O   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
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245148

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)CC(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO3/c1-6-4(8)2-3(7)5(6)9/h3,7H,2H2,1H3

> <INCHI_KEY>
NLKACWKSCREJEL-UHFFFAOYSA-N

> <FORMULA>
C5H7NO3

> <MOLECULAR_WEIGHT>
129.115

> <EXACT_MASS>
129.042593089

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
11.697750570041794

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.15

> <JCHEM_LOGP>
-1.4849539559999998

> <ALOGPS_LOGS>
0.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.194120662149732

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.890254274134925

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7206048283221156

> <JCHEM_POLAR_SURFACE_AREA>
57.61

> <JCHEM_REFRACTIVITY>
28.5163

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-1-methylpyrrolidine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

HMDB0245148
     RDKit          3D
3-Hydroxy-1-methylpyrrolidine-2,5-dione
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.1775    0.0323    0.0511 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7302    0.1216   -0.0682 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1190    0.9490    0.7140 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1749    1.6575    1.7056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4813    0.8330    0.1374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4464   -0.5771   -0.4142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4347   -1.4379    0.6908 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0877   -0.6166   -1.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -1.1213   -2.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6442    0.6554   -0.7497 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5426   -1.0036   -0.1333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5129    0.3190    1.0563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2773    1.0063    0.8569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5344    1.5152   -0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2425   -0.7882   -1.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5240   -1.5447    1.0652 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
  6  8  1  0
  8  9  2  0
  8  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
M  END
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PDB for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

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       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    6                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

COMPND    HMDB0245148
HETATM    1  C1  UNL     1       2.178   0.032   0.051  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.730   0.122  -0.068  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.119   0.949   0.714  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.175   1.658   1.706  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.481   0.833   0.137  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.446  -0.577  -0.414  1.00  0.00           C  
HETATM    7  O2  UNL     1      -1.435  -1.438   0.691  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.088  -0.617  -1.003  1.00  0.00           C  
HETATM    9  O3  UNL     1       0.365  -1.121  -2.030  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.644   0.655  -0.750  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.543  -1.004  -0.133  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.513   0.319   1.056  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.277   1.006   0.857  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.534   1.515  -0.761  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.242  -0.788  -1.118  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.524  -1.545   1.065  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    8
CONECT    3    4    4    5
CONECT    5    6   13   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9    9
END
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SMILES for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

CN1C(=O)CC(O)C1=O
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INCHI for HMDB0245148 (3-Hydroxy-1-methylpyrrolidine-2,5-dione)

InChI=1S/C5H7NO3/c1-6-4(8)2-3(7)5(6)9/h3,7H,2H2,1H3
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Synonyms
ValueSource
2-HMSIHMDB
2-Hydroxy-N-methylsuccinimideHMDB
Chemical FormulaC5H7NO3
Average Molecular Weight129.115
Monoisotopic Molecular Weight129.042593089
IUPAC Name3-hydroxy-1-methylpyrrolidine-2,5-dione
Traditional Name3-hydroxy-1-methylpyrrolidine-2,5-dione
CAS Registry NumberNot Available
SMILES
CN1C(=O)CC(O)C1=O
InChI Identifier
InChI=1S/C5H7NO3/c1-6-4(8)2-3(7)5(6)9/h3,7H,2H2,1H3
InChI KeyNLKACWKSCREJEL-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
  • Secondary alcohol
  • Lactam
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
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 ID228926
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound260809
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 ]