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Showing metabocard for Pyrrolidine (HMDB0031641)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:44:35 UTC
Update Date2023-02-21 17:21:05 UTC
HMDB IDHMDB0031641
Secondary Accession Numbers
  • HMDB31641
Metabolite Identification
Common NamePyrrolidine
DescriptionPyrrolidine is found in alcoholic beverages. Pyrrolidine is widely distributed in foodstuffs in trace amts., presumably as bacterial decarboxylation produced of proline. Pyrrolidine is present in bread, milk, cheese, carrots, celery stalks, beer, spirits, coffee, caviar and fatty fish. Pyrrolidine is a flavouring agent.Pyrrolidine is a clear liquid with an unpleasant odor that is ammoniacal, fishy, shellfish-like and seaweed-like. Pyrrolidine is found naturally in the leaves of tobacco and carrot. The pyrrolidine ring structure is present in numerous natural alkaloids such as nicotine and hygrine. It is found in many pharmaceutical drugs such as procyclidine and bepridil. It also forms the basis for the racetam compounds (e.g. piracetam, aniracetam). Pyrrolidine is a pyrrolidine ring is the central structure of the amino acids proline and hydroxyproline. (Wikipedia ) Pyrrolidine has been found to be a metabolite in Xenorhabdus (PMID: 19598185 ).
Structure
Data?1677000065
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031641 (Pyrrolidine)

  Mrv1652303202019012D          

  5  5  0  0  0  0            999 V2000
    1.5202    0.2371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6952    0.2371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4403    1.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1077    1.5066    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7752    1.0217    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
  1  5  1  0  0  0  0
M  END
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3D MOL for HMDB0031641 (Pyrrolidine)

HMDB0031641
     RDKit          3D
Pyrrolidine
 14 14  0  0  0  0  0  0  0  0999 V2000
    0.3414   -1.1076   -0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0232   -0.5399    0.0581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8404    0.9184   -0.2991 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5113    1.2373    0.0574 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2474    0.0216    0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4953   -1.3137   -1.3195 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4730   -2.0267    0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8419   -1.0272   -0.4706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1194   -0.5782    1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895    1.5562    0.2350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9673    1.0878   -1.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5969    1.8980    0.8452 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1743    0.0766   -0.4055 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5420   -0.2026    1.2560 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  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
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3D SDF for HMDB0031641 (Pyrrolidine)

  Mrv1652303202019012D          

  5  5  0  0  0  0            999 V2000
    1.5202    0.2371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6952    0.2371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4403    1.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1077    1.5066    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7752    1.0217    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
  1  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031641

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CCNC1

> <INCHI_IDENTIFIER>
InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2

> <INCHI_KEY>
RWRDLPDLKQPQOW-UHFFFAOYSA-N

> <FORMULA>
C4H9N

> <MOLECULAR_WEIGHT>
71.121

> <EXACT_MASS>
71.073499293

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
8.57813565899375

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrrolidine

> <ALOGPS_LOGP>
0.16

> <JCHEM_LOGP>
0.212918995

> <ALOGPS_LOGS>
0.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
11.402039831164966

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
22.2344

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.91e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrrolidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0031641 (Pyrrolidine)

HMDB0031641
     RDKit          3D
Pyrrolidine
 14 14  0  0  0  0  0  0  0  0999 V2000
    0.3414   -1.1076   -0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0232   -0.5399    0.0581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8404    0.9184   -0.2991 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5113    1.2373    0.0574 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2474    0.0216    0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4953   -1.3137   -1.3195 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4730   -2.0267    0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8419   -1.0272   -0.4706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1194   -0.5782    1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895    1.5562    0.2350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9673    1.0878   -1.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5969    1.8980    0.8452 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1743    0.0766   -0.4055 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5420   -0.2026    1.2560 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  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
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PDB for HMDB0031641 (Pyrrolidine)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       2.838   0.443   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.298   0.443   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.822   1.907   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.068   2.812   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       3.314   1.907   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0031641 (Pyrrolidine)

COMPND    HMDB0031641
HETATM    1  C1  UNL     1       0.341  -1.108  -0.261  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.023  -0.540   0.058  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.840   0.918  -0.299  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.511   1.237   0.057  1.00  0.00           N  
HETATM    5  C4  UNL     1       1.247   0.022   0.203  1.00  0.00           C  
HETATM    6  H1  UNL     1       0.495  -1.314  -1.320  1.00  0.00           H  
HETATM    7  H2  UNL     1       0.473  -2.027   0.324  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.842  -1.027  -0.471  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.119  -0.578   1.174  1.00  0.00           H  
HETATM   10  H5  UNL     1      -1.589   1.556   0.235  1.00  0.00           H  
HETATM   11  H6  UNL     1      -0.967   1.088  -1.396  1.00  0.00           H  
HETATM   12  H7  UNL     1       0.597   1.898   0.845  1.00  0.00           H  
HETATM   13  H8  UNL     1       2.174   0.077  -0.405  1.00  0.00           H  
HETATM   14  H9  UNL     1       1.542  -0.203   1.256  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    8    9
CONECT    3    4   10   11
CONECT    4    5   12
CONECT    5   13   14
END
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SMILES for HMDB0031641 (Pyrrolidine)

C1CCNC1
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INCHI for HMDB0031641 (Pyrrolidine)

InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-AzacyclopentaneChEBI
AzacyclopentaneChEBI
AzolidineChEBI
ButylenimineChEBI
PerhydropyrroleChEBI
ProlamineChEBI
TetrahydropyrroleChEBI
TetramethylenimineChEBI
FEMA 3523HMDB
Pyrrolidine hydrochlorideHMDB
Chemical FormulaC4H9N
Average Molecular Weight71.121
Monoisotopic Molecular Weight71.073499293
IUPAC Namepyrrolidine
Traditional Namepyrrolidine
CAS Registry Number123-75-1
SMILES
C1CCNC1
InChI Identifier
InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2
InChI KeyRWRDLPDLKQPQOW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolidines
Sub ClassNot Available
Direct ParentPyrrolidines
Alternative Parents
Substituents
  • Pyrrolidine
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-63 °CNot Available
Boiling Point87.00 to 88.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000000 mg/L @ 20 °C (exp)The Good Scents Company Information System
LogP0.460The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB007401
KNApSAcK IDC00002037
Chemspider ID29008
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrrolidine
METLIN IDNot Available
PubChem Compound31268
PDB IDNot Available
ChEBI ID33135
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1009391
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Fleming J, Ghose A, Harrison PR: Molecular mechanisms of cancer prevention by selenium compounds. Nutr Cancer. 2001;40(1):42-9. [PubMed:11799922 ]
  2. Hong TM, Teng LJ, Shun CT, Peng MC, Tsai JC: Induced interleukin-8 expression in gliomas by tumor-associated macrophages. J Neurooncol. 2009 Jul;93(3):289-301. doi: 10.1007/s11060-008-9786-z. Epub 2009 Jan 21. [PubMed:19156359 ]
  3. Li X, Li Y, Xu W: Design, synthesis, and evaluation of novel galloyl pyrrolidine derivatives as potential anti-tumor agents. Bioorg Med Chem. 2006 Mar 1;14(5):1287-93. Epub 2005 Oct 4. [PubMed:16213145 ]
  4. Lee CH, Kim SH, Lee SM: Effect of pyrrolidine dithiocarbamate on hepatic vascular stress gene expression during ischemia and reperfusion. Eur J Pharmacol. 2008 Oct 24;595(1-3):100-7. doi: 10.1016/j.ejphar.2008.07.064. Epub 2008 Aug 9. [PubMed:18722366 ]
  5. Natarajan M, Gibbons CF, Mohan S, Moore S, Kadhim MA: Oxidative stress signalling: a potential mediator of tumour necrosis factor alpha-induced genomic instability in primary vascular endothelial cells. Br J Radiol. 2007 Sep;80 Spec No 1:S13-22. [PubMed:17704321 ]
  6. Reimer D, Luxenburger E, Brachmann AO, Bode HB: A new type of pyrrolidine biosynthesis is involved in the late steps of xenocoumacin production in Xenorhabdus nematophila. Chembiochem. 2009 Aug 17;10(12):1997-2001. doi: 10.1002/cbic.200900187. [PubMed:19598185 ]
  7. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .