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Showing metabocard for Pyrrolidine-2-carbonitrile (HMDB0257000)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:39:06 UTC
Update Date2021-09-26 23:13:04 UTC
HMDB IDHMDB0257000
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyrrolidine-2-carbonitrile
Descriptionpyrrolidine-2-carbonitrile 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. Based on a literature review a significant number of articles have been published on pyrrolidine-2-carbonitrile. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyrrolidine-2-carbonitrile is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyrrolidine-2-carbonitrile 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 HMDB0257000 (Pyrrolidine-2-carbonitrile)


  Mrv1652309112119392D          

  7  7  0  0  0  0            999 V2000
    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
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   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
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    2.7643    0.0000 N   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
  3  6  1  0  0  0  0
  6  7  3  0  0  0  0
M  END
Download

3D MOL for HMDB0257000 (Pyrrolidine-2-carbonitrile)

HMDB0257000
     RDKit          3D
Pyrrolidine-2-carbonitrile
 15 15  0  0  0  0  0  0  0  0999 V2000
    3.2954    0.3870   -0.8005 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2655    0.1587   -0.3078 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9885   -0.1409    0.2840 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0537    1.0617    0.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3007    0.3999    0.1277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0382   -1.0941    0.1039 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2893   -1.1324   -0.5279 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0191   -0.4138    1.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3101    1.5077   -0.8662 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2399    1.7160    0.9723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924    0.7049    1.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9126    0.7156   -0.7315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7793   -1.6622   -0.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8691   -1.4838    1.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2309   -0.7242   -1.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  3  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
  6 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0257000 (Pyrrolidine-2-carbonitrile)


  Mrv1652309112119392D          

  7  7  0  0  0  0            999 V2000
    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
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   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
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    2.7643    0.0000 N   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
  3  6  1  0  0  0  0
  6  7  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257000

> <DATABASE_NAME>
hmdb

> <SMILES>
N#CC1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H8N2/c6-4-5-2-1-3-7-5/h5,7H,1-3H2

> <INCHI_KEY>
ALSCEGDXFJIYES-UHFFFAOYSA-N

> <FORMULA>
C5H8N2

> <MOLECULAR_WEIGHT>
96.133

> <EXACT_MASS>
96.068748266

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.410160850168467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrrolidine-2-carbonitrile

> <ALOGPS_LOGP>
-0.48

> <JCHEM_LOGP>
-0.03919254233333331

> <ALOGPS_LOGS>
-0.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
6.760036161917192

> <JCHEM_POLAR_SURFACE_AREA>
35.82

> <JCHEM_REFRACTIVITY>
27.043599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrrolidine-2-carbonitrile

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0257000 (Pyrrolidine-2-carbonitrile)

HMDB0257000
     RDKit          3D
Pyrrolidine-2-carbonitrile
 15 15  0  0  0  0  0  0  0  0999 V2000
    3.2954    0.3870   -0.8005 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2655    0.1587   -0.3078 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9885   -0.1409    0.2840 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0537    1.0617    0.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3007    0.3999    0.1277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0382   -1.0941    0.1039 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2893   -1.1324   -0.5279 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0191   -0.4138    1.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3101    1.5077   -0.8662 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2399    1.7160    0.9723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924    0.7049    1.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9126    0.7156   -0.7315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7793   -1.6622   -0.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8691   -1.4838    1.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2309   -0.7242   -1.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  3  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
  6 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0257000 (Pyrrolidine-2-carbonitrile)

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       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.060   5.160   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    3    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0257000 (Pyrrolidine-2-carbonitrile)

COMPND    HMDB0257000
HETATM    1  N1  UNL     1       3.295   0.387  -0.800  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.265   0.159  -0.308  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.988  -0.141   0.284  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.054   1.062   0.109  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.301   0.400   0.128  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.038  -1.094   0.104  1.00  0.00           C  
HETATM    7  N2  UNL     1       0.289  -1.132  -0.528  1.00  0.00           N  
HETATM    8  H1  UNL     1       1.019  -0.414   1.340  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.310   1.508  -0.866  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.240   1.716   0.972  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.792   0.705   1.086  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.913   0.716  -0.732  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.779  -1.662  -0.452  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.869  -1.484   1.147  1.00  0.00           H  
HETATM   15  H8  UNL     1       0.231  -0.724  -1.486  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    7    8
CONECT    4    5    9   10
CONECT    5    6   11   12
CONECT    6    7   13   14
CONECT    7   15
END
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SMILES for HMDB0257000 (Pyrrolidine-2-carbonitrile)

N#CC1CCCN1
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INCHI for HMDB0257000 (Pyrrolidine-2-carbonitrile)

InChI=1S/C5H8N2/c6-4-5-2-1-3-7-5/h5,7H,1-3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H8N2
Average Molecular Weight96.133
Monoisotopic Molecular Weight96.068748266
IUPAC Namepyrrolidine-2-carbonitrile
Traditional Namepyrrolidine-2-carbonitrile
CAS Registry NumberNot Available
SMILES
N#CC1CCCN1
InChI Identifier
InChI=1S/C5H8N2/c6-4-5-2-1-3-7-5/h5,7H,1-3H2
InChI KeyALSCEGDXFJIYES-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
  • Alpha-aminonitrile
  • Azacycle
  • Secondary amine
  • Nitrile
  • Carbonitrile
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Cyanide
  • 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
logP-0.48ALOGPS
logP-0.039ChemAxon
logS-0.44ALOGPS
pKa (Strongest Basic)6.76ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area35.82 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.04 m³·mol⁻¹ChemAxon
Polarizability10.41 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]+119.3530932474
DeepCCS[M-H]-116.77930932474
DeepCCS[M-2H]-152.92130932474
DeepCCS[M+Na]+127.59530932474
AllCCS[M+H]+120.332859911
AllCCS[M+H-H2O]+115.332859911
AllCCS[M+NH4]+125.032859911
AllCCS[M+Na]+126.332859911
AllCCS[M-H]-119.632859911
AllCCS[M+Na-2H]-122.632859911
AllCCS[M+HCOO]-126.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pyrrolidine-2-carbonitrileN#CC1CCCN11555.5Standard polar33892256
Pyrrolidine-2-carbonitrileN#CC1CCCN1872.1Standard non polar33892256
Pyrrolidine-2-carbonitrileN#CC1CCCN11136.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pyrrolidine-2-carbonitrile,1TMS,isomer #1C[Si](C)(C)N1CCCC1C#N1127.9Semi standard non polar33892256
Pyrrolidine-2-carbonitrile,1TMS,isomer #1C[Si](C)(C)N1CCCC1C#N1170.4Standard non polar33892256
Pyrrolidine-2-carbonitrile,1TMS,isomer #1C[Si](C)(C)N1CCCC1C#N1840.8Standard polar33892256
Pyrrolidine-2-carbonitrile,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCC1C#N1362.1Semi standard non polar33892256
Pyrrolidine-2-carbonitrile,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCC1C#N1401.4Standard non polar33892256
Pyrrolidine-2-carbonitrile,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCC1C#N2091.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyrrolidine-2-carbonitrile GC-MS (Non-derivatized) - 70eV, Positivesplash10-014j-9000000000-6a4cc8646f4a7718f63e2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyrrolidine-2-carbonitrile GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart 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 ID3900087
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ]