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Showing metabocard for 2-Pyrrolidinone (HMDB0002039)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
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
Download

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
Download

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

$$$$
Download

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
Download

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
ValueSource
1-Azacyclopentan-2-oneChEBI
2-KetopyrrolidineChEBI
2-OxopyrrolidineChEBI
2-PyrrolidoneChEBI
4-Aminobutyric acid lactamChEBI
alpha-PyrrolidinoneChEBI
alpha-PyrrolidoneChEBI
ButyrolactamChEBI
gamma-Aminobutyric acid lactamChEBI
gamma-Aminobutyric lactamChEBI
gamma-ButyrolactamChEBI
PyrrolidinoneChEBI
PyrrolidoneChEBI
4-Aminobutyrate lactamGenerator
a-PyrrolidinoneGenerator
Α-pyrrolidinoneGenerator
a-PyrrolidoneGenerator
Α-pyrrolidoneGenerator
g-Aminobutyrate lactamGenerator
g-Aminobutyric acid lactamGenerator
gamma-Aminobutyrate lactamGenerator
Γ-aminobutyrate lactamGenerator
Γ-aminobutyric acid lactamGenerator
g-Aminobutyric lactamGenerator
Γ-aminobutyric lactamGenerator
g-ButyrolactamGenerator
Γ-butyrolactamGenerator
2-Pyrrolidone, hydrotribromideHMDB
2-Pyrrolidone, rubidium saltHMDB
2-Pyrrolidone, (18)O-labeledHMDB
2-Pyrrolidone, 5-(14)C-labeledHMDB
2-Pyrrolidone, potassium saltHMDB
2-Pyrrolidone, sodium saltHMDB
2-Pyrrolidone, aluminum saltHMDB
2-Pyrrolidone, cerium saltHMDB
2-Pyrrolidone, hydrobromideHMDB
2-Pyrrolidone, hydrochlorideHMDB
2-Pyrrolidone, lithium saltHMDB
1-Methyl-2-pyrrolidinoneHMDB
2-Pyrol4-aminobutyric acid lactamHMDB
2-Pyrrolidone for synthesisHMDB
2-Pyrrolidone-butyrolactamHMDB
Aminobutyric acid lactamHMDB
Aminobutyric lactamHMDB
AminobutyrolactamHMDB
N-Methyl-2-pyrrolidinoneHMDB
Pyrrolidin-2-oneHMDB
PyrrolidonHMDB
Pyrrolidone-2HMDB
TetrahydropyrroloneHMDB
2-PyrrolidinoneChEBI
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
PropertyValueSource
Water Solubility537 g/LALOGPS
logP-0.9ALOGPS
logP-0.58ChemAxon
logS0.8ALOGPS
pKa (Strongest Acidic)14.75ChemAxon
pKa (Strongest Basic)-1.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area29.1 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity22.26 m³·mol⁻¹ChemAxon
Polarizability8.7 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
DarkChem[M+H]+115.4131661259
DarkChem[M-H]-107.83531661259
DeepCCS[M+H]+121.2630932474
DeepCCS[M-H]-118.92930932474
DeepCCS[M-2H]-154.85930932474
DeepCCS[M+Na]+129.35830932474
AllCCS[M+H]+117.532859911
AllCCS[M+H-H2O]+112.332859911
AllCCS[M+NH4]+122.332859911
AllCCS[M+Na]+123.732859911
AllCCS[M-H]-118.132859911
AllCCS[M+Na-2H]-121.932859911
AllCCS[M+HCOO]-126.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.86 minutes32390414
Predicted by Siyang on May 30, 20228.4783 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.4 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid943.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid324.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid101.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid224.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid76.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid238.2 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid304.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)293.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid633.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid158.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid793.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid214.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid244.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate536.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA256.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water168.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-PyrrolidinoneO=C1CCCN11856.1Standard polar33892256
2-PyrrolidinoneO=C1CCCN1996.5Standard non polar33892256
2-PyrrolidinoneO=C1CCCN11072.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Pyrrolidinone,1TMS,isomer #1C[Si](C)(C)N1CCCC1=O1167.9Semi standard non polar33892256
2-Pyrrolidinone,1TMS,isomer #1C[Si](C)(C)N1CCCC1=O1120.2Standard non polar33892256
2-Pyrrolidinone,1TMS,isomer #1C[Si](C)(C)N1CCCC1=O1456.2Standard polar33892256
2-Pyrrolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCC1=O1373.6Semi standard non polar33892256
2-Pyrrolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCC1=O1384.1Standard non polar33892256
2-Pyrrolidinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCC1=O1648.8Standard polar33892256
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
  1. Petroff OA, Hyder F, Mattson RH, Rothman DL: Topiramate increases brain GABA, homocarnosine, and pyrrolidinone in patients with epilepsy. Neurology. 1999 Feb;52(3):473-8. [PubMed:10025774 ]
  2. Sun X, Qiao H, Jiang H, Zhi X, Liu F, Wang J, Liu M, Dong D, Kanwar JR, Xu R, Krissansen GW: Intramuscular delivery of antiangiogenic genes suppresses secondary metastases after removal of primary tumors. Cancer Gene Ther. 2005 Jan;12(1):35-45. [PubMed:15486558 ]
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