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Showing metabocard for Propargylamine (HMDB0256820)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:24:23 UTC
Update Date2021-09-26 23:12:47 UTC
HMDB IDHMDB0256820
Secondary Accession NumbersNone
Metabolite Identification
Common NamePropargylamine
Descriptionprop-2-yn-1-amine belongs to the class of organic compounds known as acetylides. Acetylides are compounds arising by replacement of one or both hydrogen atoms of acetylene (ethyne) by a metal or other cationic group. E.g. NaC#CH monosodium acetylide. By extension, analogous compounds derived from terminal acetylenes, RC#CH. The class is limited here to derivatives of acetylene where the hydrogen atom is replaced with an element with similar or lower electronegativity that carbon. Based on a literature review a significant number of articles have been published on prop-2-yn-1-amine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Propargylamine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Propargylamine 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 HMDB0256820 (Propargylamine)


  Mrv0541 05041410402D          

  4  3  0  0  0  0            999 V2000
    1.6500   -1.4289    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  END
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3D MOL for HMDB0256820 (Propargylamine)

HMDB0256820
     RDKit          3D
Propargylamine
  9  8  0  0  0  0  0  0  0  0999 V2000
    2.1156   -0.0368    0.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9244   -0.2651    0.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5030   -0.5311    0.0539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3073    0.6516   -0.0538 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1659    0.1592    0.1469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7233   -1.1525   -0.8418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8439   -1.0952    0.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0060    0.7815    0.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8224    1.4883   -0.3860 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
  1  5  1  0
  3  6  1  0
  3  7  1  0
  4  8  1  0
  4  9  1  0
M  END
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3D SDF for HMDB0256820 (Propargylamine)


  Mrv0541 05041410402D          

  4  3  0  0  0  0            999 V2000
    1.6500   -1.4289    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256820

> <DATABASE_NAME>
hmdb

> <SMILES>
NCC#C

> <INCHI_IDENTIFIER>
InChI=1S/C3H5N/c1-2-3-4/h1H,3-4H2

> <INCHI_KEY>
JKANAVGODYYCQF-UHFFFAOYSA-N

> <FORMULA>
C3H5N

> <MOLECULAR_WEIGHT>
55.0785

> <EXACT_MASS>
55.042199165

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
6.235665236019316

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
prop-2-yn-1-amine

> <ALOGPS_LOGP>
-0.72

> <JCHEM_LOGP>
-0.3973758193333333

> <ALOGPS_LOGS>
-1.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.97304181010972

> <JCHEM_POLAR_SURFACE_AREA>
26.02

> <JCHEM_REFRACTIVITY>
17.499

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-propynylamine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0256820 (Propargylamine)

HMDB0256820
     RDKit          3D
Propargylamine
  9  8  0  0  0  0  0  0  0  0999 V2000
    2.1156   -0.0368    0.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9244   -0.2651    0.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5030   -0.5311    0.0539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3073    0.6516   -0.0538 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1659    0.1592    0.1469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7233   -1.1525   -0.8418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8439   -1.0952    0.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0060    0.7815    0.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8224    1.4883   -0.3860 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
  1  5  1  0
  3  6  1  0
  3  7  1  0
  4  8  1  0
  4  9  1  0
M  END
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PDB for HMDB0256820 (Propargylamine)

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0256820 (Propargylamine)

COMPND    HMDB0256820
HETATM    1  C1  UNL     1       2.116  -0.037   0.126  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.924  -0.265   0.088  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.503  -0.531   0.054  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.307   0.652  -0.054  1.00  0.00           N  
HETATM    5  H1  UNL     1       3.166   0.159   0.147  1.00  0.00           H  
HETATM    6  H2  UNL     1      -0.723  -1.153  -0.842  1.00  0.00           H  
HETATM    7  H3  UNL     1      -0.844  -1.095   0.971  1.00  0.00           H  
HETATM    8  H4  UNL     1      -2.006   0.782   0.679  1.00  0.00           H  
HETATM    9  H5  UNL     1      -0.822   1.488  -0.386  1.00  0.00           H  
CONECT    1    2    2    2    5
CONECT    2    3
CONECT    3    4    6    7
CONECT    4    8    9
END
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SMILES for HMDB0256820 (Propargylamine)

NCC#C
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INCHI for HMDB0256820 (Propargylamine)

InChI=1S/C3H5N/c1-2-3-4/h1H,3-4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Propargylamine monohydrochlorideMeSH
PropinylamineMeSH
Chemical FormulaC3H5N
Average Molecular Weight55.0785
Monoisotopic Molecular Weight55.042199165
IUPAC Nameprop-2-yn-1-amine
Traditional Name2-propynylamine
CAS Registry NumberNot Available
SMILES
NCC#C
InChI Identifier
InChI=1S/C3H5N/c1-2-3-4/h1H,3-4H2
InChI KeyJKANAVGODYYCQF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as acetylides. Acetylides are compounds arising by replacement of one or both hydrogen atoms of acetylene (ethyne) by a metal or other cationic group. E.G. NaC#CH monosodium acetylide. By extension, analogous compounds derived from terminal acetylenes, RC#CH. The class is limited here to derivatives of acetylene where the hydrogen atom is replaced with an element with similar or lower electronegativity that carbon.
KingdomOrganic compounds
Super ClassAcetylides
ClassNot Available
Sub ClassNot Available
Direct ParentAcetylides
Alternative Parents
Substituents
  • Acetylide
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-0.72ALOGPS
logP-0.4ChemAxon
logS-1.6ALOGPS
pKa (Strongest Basic)8.97ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area26.02 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity17.5 m³·mol⁻¹ChemAxon
Polarizability6.24 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
DeepCCS[M+H]+116.18630932474
DeepCCS[M-H]-114.39430932474
DeepCCS[M-2H]-149.6530932474
DeepCCS[M+Na]+123.22230932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PropargylamineNCC#C1019.2Standard polar33892256
PropargylamineNCC#C534.0Standard non polar33892256
PropargylamineNCC#C506.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Propargylamine,1TMS,isomer #1C#CCN[Si](C)(C)C840.3Semi standard non polar33892256
Propargylamine,1TMS,isomer #1C#CCN[Si](C)(C)C762.1Standard non polar33892256
Propargylamine,1TMS,isomer #1C#CCN[Si](C)(C)C1176.8Standard polar33892256
Propargylamine,2TMS,isomer #1C#CCN([Si](C)(C)C)[Si](C)(C)C1088.1Semi standard non polar33892256
Propargylamine,2TMS,isomer #1C#CCN([Si](C)(C)C)[Si](C)(C)C1011.0Standard non polar33892256
Propargylamine,2TMS,isomer #1C#CCN([Si](C)(C)C)[Si](C)(C)C1100.1Standard polar33892256
Propargylamine,1TBDMS,isomer #1C#CCN[Si](C)(C)C(C)(C)C1060.9Semi standard non polar33892256
Propargylamine,1TBDMS,isomer #1C#CCN[Si](C)(C)C(C)(C)C1002.7Standard non polar33892256
Propargylamine,1TBDMS,isomer #1C#CCN[Si](C)(C)C(C)(C)C1311.9Standard polar33892256
Propargylamine,2TBDMS,isomer #1C#CCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C1429.7Semi standard non polar33892256
Propargylamine,2TBDMS,isomer #1C#CCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C1421.4Standard non polar33892256
Propargylamine,2TBDMS,isomer #1C#CCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C1321.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Propargylamine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-9000000000-c2794fc7b21341a94bfa2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Propargylamine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 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, 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 NMR13C NMR Spectrum (1D, 300 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 NMR1H NMR Spectrum (1D, 400 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 NMR13C NMR Spectrum (1D, 500 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, 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 NMR1H NMR Spectrum (1D, 700 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, 800 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, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C 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 ID208829
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 ]