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Showing metabocard for 1-Methylpyrrolidine (HMDB0243946)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:09:20 UTC
Update Date2021-09-26 22:51:20 UTC
HMDB IDHMDB0243946
Secondary Accession NumbersNone
Metabolite Identification
Common Name1-Methylpyrrolidine
Description1-METHYLPYRROLIDINE, also known as N-methylpyrrolidine, belongs to the class of organic compounds known as n-alkylpyrrolidines. N-alkylpyrrolidines are compounds containing a pyrrolidine moiety that is substituted at the N1-position with an alkyl group. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. 1-METHYLPYRROLIDINE is a very strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-methylpyrrolidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-Methylpyrrolidine 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 HMDB0243946 (1-Methylpyrrolidine)


  Mrv1533004201503592D          

  6  6  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
    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
  1  2  1  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  6  1  0  0  0  0
  2  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0243946 (1-Methylpyrrolidine)

HMDB0243946
     RDKit          3D
1-Methylpyrrolidine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.8626    0.0426    0.0702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6596    0.2851   -0.7366 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1971    1.2536   -0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4803    0.5141    0.2729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8927   -0.8892    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0889   -0.9513   -0.8238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -0.9121   -0.2243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5675    0.8768   -0.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6222    0.0187    1.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718    2.1002   -0.7172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3085    1.5996    0.8390 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0833    0.4570   -0.6362 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9689    0.9017    1.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6490   -1.6658    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2120   -0.8934    1.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5207   -1.8471   -0.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8358   -0.8904   -1.6466 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
M  END
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3D SDF for HMDB0243946 (1-Methylpyrrolidine)


  Mrv1533004201503592D          

  6  6  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
    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
  1  2  1  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  6  1  0  0  0  0
  2  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0243946

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H11N/c1-6-4-2-3-5-6/h2-5H2,1H3

> <INCHI_KEY>
AVFZOVWCLRSYKC-UHFFFAOYSA-N

> <FORMULA>
C5H11N

> <MOLECULAR_WEIGHT>
85.15

> <EXACT_MASS>
85.089149358

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
10.497550285472068

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methylpyrrolidine

> <ALOGPS_LOGP>
0.54

> <JCHEM_LOGP>
0.5959669323333334

> <ALOGPS_LOGS>
0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.077383506499574

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
27.529099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyl-pyrrolidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0243946 (1-Methylpyrrolidine)

HMDB0243946
     RDKit          3D
1-Methylpyrrolidine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.8626    0.0426    0.0702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6596    0.2851   -0.7366 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1971    1.2536   -0.0867 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4803    0.5141    0.2729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8927   -0.8892    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0889   -0.9513   -0.8238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -0.9121   -0.2243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5675    0.8768   -0.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6222    0.0187    1.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718    2.1002   -0.7172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3085    1.5996    0.8390 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0833    0.4570   -0.6362 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9689    0.9017    1.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6490   -1.6658    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2120   -0.8934    1.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5207   -1.8471   -0.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8358   -0.8904   -1.6466 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
M  END
Download

PDB for HMDB0243946 (1-Methylpyrrolidine)

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         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  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0243946 (1-Methylpyrrolidine)

COMPND    HMDB0243946
HETATM    1  C1  UNL     1      -1.863   0.043   0.070  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.660   0.285  -0.737  1.00  0.00           N  
HETATM    3  C2  UNL     1       0.197   1.254  -0.087  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.480   0.514   0.273  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.893  -0.889   0.485  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.089  -0.951  -0.824  1.00  0.00           C  
HETATM    7  H1  UNL     1      -2.339  -0.912  -0.224  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.567   0.877  -0.083  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.622   0.019   1.155  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.472   2.100  -0.717  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.309   1.600   0.839  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.083   0.457  -0.636  1.00  0.00           H  
HETATM   13  H7  UNL     1       1.969   0.902   1.158  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.649  -1.666   0.470  1.00  0.00           H  
HETATM   15  H9  UNL     1       0.212  -0.893   1.346  1.00  0.00           H  
HETATM   16  H10 UNL     1      -0.521  -1.847  -0.842  1.00  0.00           H  
HETATM   17  H11 UNL     1       0.836  -0.890  -1.647  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    6
CONECT    3    4   10   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6   16   17
END
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SMILES for HMDB0243946 (1-Methylpyrrolidine)

CN1CCCC1
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INCHI for HMDB0243946 (1-Methylpyrrolidine)

InChI=1S/C5H11N/c1-6-4-2-3-5-6/h2-5H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
N-Methylpyrrolidine hydrobromideMeSH
Methylpyrrolidinium bromideMeSH
N-MethylpyrrolidineMeSH
N-Methylpyrrolidine hydrochlorideMeSH
Chemical FormulaC5H11N
Average Molecular Weight85.15
Monoisotopic Molecular Weight85.089149358
IUPAC Name1-methylpyrrolidine
Traditional Name1-methyl-pyrrolidine
CAS Registry NumberNot Available
SMILES
CN1CCCC1
InChI Identifier
InChI=1S/C5H11N/c1-6-4-2-3-5-6/h2-5H2,1H3
InChI KeyAVFZOVWCLRSYKC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-alkylpyrrolidines. N-alkylpyrrolidines are compounds containing a pyrrolidine moiety that is substituted at the N1-position with an alkyl group. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolidines
Sub ClassN-alkylpyrrolidines
Direct ParentN-alkylpyrrolidines
Alternative Parents
Substituents
  • N-alkylpyrrolidine
  • Tertiary aliphatic amine
  • Tertiary amine
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
PropertyValueSource
logP0.54ALOGPS
logP0.6ChemAxon
logS0.62ALOGPS
pKa (Strongest Basic)10.08ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area3.24 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.53 m³·mol⁻¹ChemAxon
Polarizability10.5 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]+122.70630932474
DeepCCS[M-H]-120.68830932474
DeepCCS[M-2H]-156.08130932474
DeepCCS[M+Na]+130.57630932474
AllCCS[M+H]+114.832859911
AllCCS[M+H-H2O]+109.632859911
AllCCS[M+NH4]+119.632859911
AllCCS[M+Na]+121.032859911
AllCCS[M-H]-122.632859911
AllCCS[M+Na-2H]-126.532859911
AllCCS[M+HCOO]-130.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-MethylpyrrolidineCN1CCCC1867.5Standard polar33892256
1-MethylpyrrolidineCN1CCCC1666.0Standard non polar33892256
1-MethylpyrrolidineCN1CCCC1663.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1-Methylpyrrolidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-003u-9000000000-6c4ee68ffe45af4266e12021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Methylpyrrolidine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 1-Methylpyrrolidine 30V, Positive-QTOFsplash10-0002-9000000000-2a546f74b163862746ae2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 1-Methylpyrrolidine 0V, Positive-QTOFsplash10-004i-9000000000-d47c135c4a01c36913d22021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 1-Methylpyrrolidine 10V, Positive-QTOFsplash10-004i-9000000000-5d0b1c0de258ded696f82021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 10V, Positive-QTOFsplash10-000i-9000000000-16173c27a1d61ee4d1162016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 20V, Positive-QTOFsplash10-000i-9000000000-0e5866017b78af3cea272016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 40V, Positive-QTOFsplash10-0abc-9000000000-86bb1eb5391d7bf3e4062016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 10V, Negative-QTOFsplash10-001i-9000000000-780173f549770c829ab92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 20V, Negative-QTOFsplash10-001i-9000000000-a1f9b4cfff0e8583476c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 40V, Negative-QTOFsplash10-066r-9000000000-db5651c1e8b046c883462016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 10V, Positive-QTOFsplash10-000i-9000000000-0bbed6312313e26c10122021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 20V, Positive-QTOFsplash10-000i-9000000000-f053b4cb7f0b62aabc502021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 40V, Positive-QTOFsplash10-001r-9000000000-29291eaf886b7126cd352021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 10V, Negative-QTOFsplash10-001i-9000000000-2fea16a68b3c786610582021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 20V, Negative-QTOFsplash10-001i-9000000000-2fea16a68b3c786610582021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Methylpyrrolidine 40V, Negative-QTOFsplash10-001l-9000000000-123f79f423bf7c9364432021-10-12Wishart 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 Compound8454
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 ]