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Showing metabocard for 2-Pyrrolidinone (HMDB0002039)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:33 UTC
Update Date2023-02-21 17:16:05 UTC
HMDB IDHMDB0002039
Secondary Accession Numbers
  • HMDB02039
Metabolite Identification
Common Name2-Pyrrolidinone
Description2-Pyrrolidinone is a lactam cyclization product of gamma-aminobutyric acid (GABA) (PMID 10332870 ). Vigabatrin (VGB, an antiepileptic drug) increases human brain gamma-aminobutyric acid (GABA) and the related metabolites, including 2-pyrrolidinone. Patients taking VGB are expected to have an increase of these metabolites (PMID 10403220 , 10840398 ). 2-Pyrrolidone is an organic compound consisting of a five-membered lactam. It is a colorless liquid which is used in industrial settings as a high-boiling non-corrosive polar solvent for a wide variety of applications. It is miscible with a wide variety of other solvents including water, ethanol, diethyl ether, chloroform, benzene, ethyl acetate and carbon disulfide.
Structure
Data?1676999765
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002039 (2-Pyrrolidinone)

  Mrv1652305261923552D          

  6  6  0  0  0  0            999 V2000
   18.7986   -4.4667    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3466   -4.6966    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.6791   -4.2117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9340   -3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7591   -3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0140   -4.2117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0002039 (2-Pyrrolidinone)

HMDB0002039
     RDKit          3D
2-Pyrrolidinone
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.4986    2.4344    0.7192 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1972    1.2474    0.4487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1004    0.0686    0.4867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4654   -0.7911   -0.6029 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9952   -0.6655   -0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0810    0.7760    0.0456 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1446    0.3341    0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0280   -0.4571    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8337   -1.8102   -0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6220   -0.2460   -1.5579 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1998   -1.2614    0.6815 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6567   -0.9463   -1.0650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9571    1.3171   -0.0480 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  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
M  END
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3D SDF for HMDB0002039 (2-Pyrrolidinone)

  Mrv1652305261923552D          

  6  6  0  0  0  0            999 V2000
   18.7986   -4.4667    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3466   -4.6966    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.6791   -4.2117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9340   -3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7591   -3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0140   -4.2117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002039

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6)

> <INCHI_KEY>
HNJBEVLQSNELDL-UHFFFAOYSA-N

> <FORMULA>
C4H7NO

> <MOLECULAR_WEIGHT>
85.1045

> <EXACT_MASS>
85.052763851

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.701938043572053

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrrolidin-2-one

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.5796092983333335

> <ALOGPS_LOGS>
0.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.745904083510304

> <JCHEM_PKA_STRONGEST_BASIC>
-1.826277890342777

> <JCHEM_POLAR_SURFACE_AREA>
29.1

> <JCHEM_REFRACTIVITY>
22.2579

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.37e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrrolidone

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002039 (2-Pyrrolidinone)

HMDB0002039
     RDKit          3D
2-Pyrrolidinone
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.4986    2.4344    0.7192 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1972    1.2474    0.4487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1004    0.0686    0.4867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4654   -0.7911   -0.6029 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9952   -0.6655   -0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0810    0.7760    0.0456 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1446    0.3341    0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0280   -0.4571    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8337   -1.8102   -0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6220   -0.2460   -1.5579 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1998   -1.2614    0.6815 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6567   -0.9463   -1.0650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9571    1.3171   -0.0480 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  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
M  END
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PDB for HMDB0002039 (2-Pyrrolidinone)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      35.091  -8.338   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0      32.380  -8.767   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      31.134  -7.862   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      31.610  -6.397   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      33.150  -6.397   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.626  -7.862   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    3    6                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    2    5                                                  
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0002039 (2-Pyrrolidinone)

COMPND    HMDB0002039
HETATM    1  O1  UNL     1      -0.499   2.434   0.719  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.197   1.247   0.449  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.100   0.069   0.487  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.465  -0.791  -0.603  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.995  -0.666  -0.239  1.00  0.00           C  
HETATM    6  N1  UNL     1       1.081   0.776   0.046  1.00  0.00           N  
HETATM    7  H1  UNL     1      -2.145   0.334   0.249  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.028  -0.457   1.483  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.834  -1.810  -0.601  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.622  -0.246  -1.558  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.200  -1.261   0.682  1.00  0.00           H  
HETATM   12  H6  UNL     1       1.657  -0.946  -1.065  1.00  0.00           H  
HETATM   13  H7  UNL     1       1.957   1.317  -0.048  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    7    8
CONECT    4    5    9   10
CONECT    5    6   11   12
CONECT    6   13
END
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SMILES for HMDB0002039 (2-Pyrrolidinone)

O=C1CCCN1
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INCHI for HMDB0002039 (2-Pyrrolidinone)

InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H7NO
Average Molecular Weight85.1045
Monoisotopic Molecular Weight85.052763851
IUPAC Namepyrrolidin-2-one
Traditional Namepyrrolidone
CAS Registry Number616-45-5
SMILES
O=C1CCCN1
InChI Identifier
InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6)
InChI KeyHNJBEVLQSNELDL-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
  • Secondary carboxylic acid amide
  • Lactam
  • Carboxamide group
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point23 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mL at 20 °CNot Available
LogP-0.85SASAKI,H ET AL. (1991)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
Tissue Locations
  • Brain
  • Epidermis
  • Skeletal Muscle
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0975 +/- 0.0300 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified4.23 (0.0-26.0) uMAdult (>18 years old)Both
Bladder infections		 details
Associated Disorders and Diseases
Disease References
Bladder infections
  1. Tricker AR, Pfundstein B, Kalble T, Preussmann R: Secondary amine precursors to nitrosamines in human saliva, gastric juice, blood, urine and faeces. Carcinogenesis. 1992 Apr;13(4):563-8. [PubMed:1576707 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000741
KNApSAcK IDC00038233
Chemspider ID11530
KEGG Compound IDC11118
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Pyrrolidone
METLIN ID6452
PubChem Compound12025
PDB IDNot Available
ChEBI ID36592
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References