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Showing metabocard for Cyclopentylamine (HMDB0250671)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:46:00 UTC
Update Date2021-09-26 23:02:16 UTC
HMDB IDHMDB0250671
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyclopentylamine
Descriptioncyclopentanamine belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing an primary aliphatic amine group. Based on a literature review a small amount of articles have been published on cyclopentanamine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyclopentylamine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyclopentylamine 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 HMDB0250671 (Cyclopentylamine)


  Mrv0541 05031419502D          

  6  6  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
    0.9803   -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
    1.2352    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
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
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3D MOL for HMDB0250671 (Cyclopentylamine)

HMDB0250671
     RDKit          3D
Cyclopentylamine
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.0639   -0.5788   -0.5085 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7479   -0.0426   -0.6694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2342   -1.1338   -0.2332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5125   -0.3962    0.0412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0938    0.9686    0.5448 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4153    1.0507    0.3174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8243    0.0990   -0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0999   -1.3588    0.1704 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5196    0.3294   -1.6783 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1836   -1.5147    0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3074   -1.9001   -1.0005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1615   -0.3258   -0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0663   -0.9725    0.8145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6363    1.7533   -0.0216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3638    1.0615    1.6029 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6037    2.0575   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9176    0.9034    1.2863 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
  2  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 HMDB0250671 (Cyclopentylamine)


  Mrv0541 05031419502D          

  6  6  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
    0.9803   -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
    1.2352    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
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250671

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H11N/c6-5-3-1-2-4-5/h5H,1-4,6H2

> <INCHI_KEY>
NISGSNTVMOOSJQ-UHFFFAOYSA-N

> <FORMULA>
C5H11N

> <MOLECULAR_WEIGHT>
85.1475

> <EXACT_MASS>
85.089149357

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.57678361656565

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopentanamine

> <ALOGPS_LOGP>
0.85

> <JCHEM_LOGP>
0.7292430013333332

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.45484241595921

> <JCHEM_POLAR_SURFACE_AREA>
26.02

> <JCHEM_REFRACTIVITY>
26.332

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.35e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentanamine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0250671 (Cyclopentylamine)

HMDB0250671
     RDKit          3D
Cyclopentylamine
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.0639   -0.5788   -0.5085 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7479   -0.0426   -0.6694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2342   -1.1338   -0.2332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5125   -0.3962    0.0412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0938    0.9686    0.5448 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4153    1.0507    0.3174 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8243    0.0990   -0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0999   -1.3588    0.1704 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5196    0.3294   -1.6783 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1836   -1.5147    0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3074   -1.9001   -1.0005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1615   -0.3258   -0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0663   -0.9725    0.8145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6363    1.7533   -0.0216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3638    1.0615    1.6029 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6037    2.0575   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9176    0.9034    1.2863 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
  2  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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PDB for HMDB0250671 (Cyclopentylamine)

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    5                                                       
CONECT    5    3    4    6                                                  
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0250671 (Cyclopentylamine)

COMPND    HMDB0250671
HETATM    1  N1  UNL     1       2.064  -0.579  -0.508  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.748  -0.043  -0.669  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.234  -1.134  -0.233  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.513  -0.396   0.041  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.094   0.969   0.545  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.415   1.051   0.317  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.824   0.099  -0.461  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.100  -1.359   0.170  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.520   0.329  -1.678  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.184  -1.515   0.741  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.307  -1.900  -1.000  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.161  -0.326  -0.854  1.00  0.00           H  
HETATM   13  H7  UNL     1      -2.066  -0.973   0.814  1.00  0.00           H  
HETATM   14  H8  UNL     1      -1.636   1.753  -0.022  1.00  0.00           H  
HETATM   15  H9  UNL     1      -1.364   1.061   1.603  1.00  0.00           H  
HETATM   16  H10 UNL     1       0.604   2.058  -0.092  1.00  0.00           H  
HETATM   17  H11 UNL     1       0.918   0.903   1.286  1.00  0.00           H  
CONECT    1    2    7    8
CONECT    2    3    6    9
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 HMDB0250671 (Cyclopentylamine)

NC1CCCC1
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INCHI for HMDB0250671 (Cyclopentylamine)

InChI=1S/C5H11N/c6-5-3-1-2-4-5/h5H,1-4,6H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H11N
Average Molecular Weight85.1475
Monoisotopic Molecular Weight85.089149357
IUPAC Namecyclopentanamine
Traditional Namecyclopentanamine
CAS Registry NumberNot Available
SMILES
NC1CCCC1
InChI Identifier
InChI=1S/C5H11N/c6-5-3-1-2-4-5/h5H,1-4,6H2
InChI KeyNISGSNTVMOOSJQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing an primary aliphatic amine group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentMonoalkylamines
Alternative Parents
Substituents
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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
logP0.85ALOGPS
logP0.73ChemAxon
logS-0.56ALOGPS
pKa (Strongest Basic)10.45ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area26.02 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.33 m³·mol⁻¹ChemAxon
Polarizability10.58 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]+124.98730932474
DeepCCS[M-H]-123.00230932474
DeepCCS[M-2H]-158.38730932474
DeepCCS[M+Na]+132.76430932474
AllCCS[M+H]+120.132859911
AllCCS[M+H-H2O]+115.132859911
AllCCS[M+NH4]+124.832859911
AllCCS[M+Na]+126.232859911
AllCCS[M-H]-117.732859911
AllCCS[M+Na-2H]-121.632859911
AllCCS[M+HCOO]-125.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclopentylamineNC1CCCC11118.2Standard polar33892256
CyclopentylamineNC1CCCC1751.3Standard non polar33892256
CyclopentylamineNC1CCCC1786.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cyclopentylamine,1TMS,isomer #1C[Si](C)(C)NC1CCCC1942.4Semi standard non polar33892256
Cyclopentylamine,1TMS,isomer #1C[Si](C)(C)NC1CCCC11000.2Standard non polar33892256
Cyclopentylamine,1TMS,isomer #1C[Si](C)(C)NC1CCCC11158.6Standard polar33892256
Cyclopentylamine,2TMS,isomer #1C[Si](C)(C)N(C1CCCC1)[Si](C)(C)C1210.2Semi standard non polar33892256
Cyclopentylamine,2TMS,isomer #1C[Si](C)(C)N(C1CCCC1)[Si](C)(C)C1268.9Standard non polar33892256
Cyclopentylamine,2TMS,isomer #1C[Si](C)(C)N(C1CCCC1)[Si](C)(C)C1321.4Standard polar33892256
Cyclopentylamine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1CCCC11218.7Semi standard non polar33892256
Cyclopentylamine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1CCCC11187.1Standard non polar33892256
Cyclopentylamine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1CCCC11390.4Standard polar33892256
Cyclopentylamine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1CCCC1)[Si](C)(C)C(C)(C)C1650.2Semi standard non polar33892256
Cyclopentylamine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1CCCC1)[Si](C)(C)C(C)(C)C1647.7Standard non polar33892256
Cyclopentylamine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1CCCC1)[Si](C)(C)C(C)(C)C1567.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentylamine GC-MS (Non-derivatized) - 70eV, Positivesplash10-054x-9000000000-75e10b219dc48deb34222021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentylamine 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 - Cyclopentylamine 10V, Positive-QTOFsplash10-014r-9000000000-70eb6cb1fcc5db3f06ea2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentylamine 20V, Positive-QTOFsplash10-014i-9000000000-599a3efd766a72af5d8a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentylamine 40V, Positive-QTOFsplash10-00kf-9000000000-e470fa00061e3cfc91b42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentylamine 10V, Negative-QTOFsplash10-001i-9000000000-2fea16a68b3c786610582021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentylamine 20V, Negative-QTOFsplash10-001i-9000000000-2fea16a68b3c786610582021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentylamine 40V, Negative-QTOFsplash10-001i-9000000000-137fdf98925c8f1634ad2021-10-12Wishart 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 ID2803
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 ]