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Showing metabocard for Pentanenitrile (HMDB0040173)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:42:58 UTC
Update Date2023-02-21 17:27:49 UTC
HMDB IDHMDB0040173
Secondary Accession Numbers
  • HMDB40173
Metabolite Identification
Common NamePentanenitrile
DescriptionPentanenitrile belongs to the class of organic compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N. Pentanenitrile has been detected, but not quantified in, brassicas and corns (Zea mays). This could make pentanenitrile a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Pentanenitrile.
Structure
Data?1677000469
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040173 (Pentanenitrile)


  Mrv0541 05061311402D          

  6  5  0  0  0  0            999 V2000
   -0.1914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  3  0  0  0  0
M  END
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3D MOL for HMDB0040173 (Pentanenitrile)

HMDB0040173
     RDKit          3D
Pentanenitrile
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.1936   -0.0788   -0.0318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8130    0.4885   -0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2568   -0.3956    0.3772 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5963    0.2999    0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7095   -0.4743    0.6493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948   -1.0875    1.0903 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2326   -0.8640    0.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4811   -0.5516   -1.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9370    0.7360    0.1980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5487    0.6039   -1.3126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7201    1.4982    0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2924   -1.3804   -0.1102 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1473   -0.5298    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7515    0.4063   -0.9928 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5776    1.3291    0.5199 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  3  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
M  END
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3D SDF for HMDB0040173 (Pentanenitrile)


  Mrv0541 05061311402D          

  6  5  0  0  0  0            999 V2000
   -0.1914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040173

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC#N

> <INCHI_IDENTIFIER>
InChI=1S/C5H9N/c1-2-3-4-5-6/h2-4H2,1H3

> <INCHI_KEY>
RFFFKMOABOFIDF-UHFFFAOYSA-N

> <FORMULA>
C5H9N

> <MOLECULAR_WEIGHT>
83.1317

> <EXACT_MASS>
83.073499293

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.122576911666691

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentanenitrile

> <ALOGPS_LOGP>
1.10

> <JCHEM_LOGP>
1.4242763293333334

> <ALOGPS_LOGS>
-0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
25.4519

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
valeronitrile

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0040173 (Pentanenitrile)

HMDB0040173
     RDKit          3D
Pentanenitrile
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.1936   -0.0788   -0.0318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8130    0.4885   -0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2568   -0.3956    0.3772 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5963    0.2999    0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7095   -0.4743    0.6493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948   -1.0875    1.0903 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2326   -0.8640    0.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4811   -0.5516   -1.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9370    0.7360    0.1980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5487    0.6039   -1.3126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7201    1.4982    0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2924   -1.3804   -0.1102 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1473   -0.5298    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7515    0.4063   -0.9928 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5776    1.3291    0.5199 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  3  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
M  END
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PDB for HMDB0040173 (Pentanenitrile)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -0.357  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977  -1.334   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.311  -0.564   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0040173 (Pentanenitrile)

COMPND    HMDB0040173
HETATM    1  C1  UNL     1      -2.194  -0.079  -0.032  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.813   0.489  -0.231  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.257  -0.396   0.377  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.596   0.300   0.101  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.709  -0.474   0.649  1.00  0.00           C  
HETATM    6  N1  UNL     1       3.595  -1.088   1.090  1.00  0.00           N  
HETATM    7  H1  UNL     1      -2.233  -0.864   0.755  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.481  -0.552  -1.013  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.937   0.736   0.198  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.549   0.604  -1.313  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.720   1.498   0.221  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.292  -1.380  -0.110  1.00  0.00           H  
HETATM   13  H7  UNL     1       0.147  -0.530   1.460  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.751   0.406  -0.993  1.00  0.00           H  
HETATM   15  H9  UNL     1       1.578   1.329   0.520  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6    6    6
END
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SMILES for HMDB0040173 (Pentanenitrile)

CCCCC#N
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INCHI for HMDB0040173 (Pentanenitrile)

InChI=1S/C5H9N/c1-2-3-4-5-6/h2-4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Butyl cyanideHMDB
1-cyano-ButaneHMDB
1-CyanobutaneHMDB
Butyl cyanideHMDB
N-Butyl cyanideHMDB
N-PentanenitrileHMDB
N-ValeronitrileHMDB
Pentanenitrile, 9ciHMDB
PentanonitrileHMDB
Valeronitrile, 8ciHMDB
Chemical FormulaC5H9N
Average Molecular Weight83.1317
Monoisotopic Molecular Weight83.073499293
IUPAC Namepentanenitrile
Traditional Namevaleronitrile
CAS Registry Number110-59-8
SMILES
CCCCC#N
InChI Identifier
InChI=1S/C5H9N/c1-2-3-4-5-6/h2-4H2,1H3
InChI KeyRFFFKMOABOFIDF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassOrganic cyanides
Direct ParentNitriles
Alternative Parents
Substituents
  • Nitrile
  • Carbonitrile
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-96.2 °CNot Available
Boiling Point141.00 to 142.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility7746 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.12Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility19.9 g/LALOGPS
logP1.1ALOGPS
logP1.42ChemAxon
logS-0.62ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.79 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity25.45 m³·mol⁻¹ChemAxon
Polarizability10.12 ųChemAxon
Number of Rings0ChemAxon
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]+117.05431661259
DarkChem[M-H]-111.23431661259
DeepCCS[M+H]+126.90630932474
DeepCCS[M-H]-125.06430932474
DeepCCS[M-2H]-160.42930932474
DeepCCS[M+Na]+134.31630932474
AllCCS[M+H]+121.932859911
AllCCS[M+H-H2O]+117.532859911
AllCCS[M+NH4]+126.132859911
AllCCS[M+Na]+127.332859911
AllCCS[M-H]-129.832859911
AllCCS[M+Na-2H]-134.332859911
AllCCS[M+HCOO]-139.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PentanenitrileCCCCC#N1172.7Standard polar33892256
PentanenitrileCCCCC#N733.6Standard non polar33892256
PentanenitrileCCCCC#N762.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Pentanenitrile EI-B (Non-derivatized)splash10-004l-9000000000-5b742cee89fdaf664cfd2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Pentanenitrile EI-B (Non-derivatized)splash10-004l-9000000000-5b742cee89fdaf664cfd2018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentanenitrile GC-MS (Non-derivatized) - 70eV, Positivesplash10-002f-9000000000-c3c87667ee4eafc24b632017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentanenitrile GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 10V, Positive-QTOFsplash10-001i-9000000000-8dde79c8f6d10d0df4962016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 20V, Positive-QTOFsplash10-014i-9000000000-f351051cc7d4b427cc472016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 40V, Positive-QTOFsplash10-052f-9000000000-015ec86f2a2c529897742016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 10V, Negative-QTOFsplash10-001i-9000000000-d967574e689360ac5c4f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 20V, Negative-QTOFsplash10-001i-9000000000-72a4a231c4c8ed27e8e92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 40V, Negative-QTOFsplash10-05mo-9000000000-6bfdb4696fdefe1ecd412016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 10V, Negative-QTOFsplash10-001i-9000000000-34725d39e59b81eb78242021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 20V, Negative-QTOFsplash10-001i-9000000000-893d23a4b5dcc981b2f12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 40V, Negative-QTOFsplash10-0udi-9000000000-483a0fce91d09441167a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 10V, Positive-QTOFsplash10-0a59-9000000000-59a80cfcc1771bcfa5082021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 20V, Positive-QTOFsplash10-052f-9000000000-58bbbf2b1b8450b13f882021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentanenitrile 40V, Positive-QTOFsplash10-0006-9000000000-ca3674a5cc237298a1ac2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
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 IDFDB019884
KNApSAcK IDC00054024
Chemspider ID7770
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPentanenitrile
METLIN IDNot Available
PubChem Compound8061
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1296271
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .