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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 08:53:31 UTC

Update Date

2021-09-26 23:03:34 UTC

HMDB ID

HMDB0251529

Secondary Accession Numbers

None

Metabolite Identification

Common Name

DL-Propargylglycine

Description

2-aminopent-4-ynoic acid belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Based on a literature review a significant number of articles have been published on 2-aminopent-4-ynoic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Dl-propargylglycine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically DL-Propargylglycine 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Aminopent-4-ynoate	Generator
L-2-Amino-4-pentynoic acid	MeSH
Propargylglycine hydrochloride	MeSH
Propargylglycine, (+-)-isomer	MeSH
Propargylglycine, (R)-isomer	MeSH
Propargylglycine, (S)-isomer	MeSH
Propargylglycine	MeSH

Chemical Formula

C₅H₇NO₂

Average Molecular Weight

113.116

Monoisotopic Molecular Weight

113.047678469

IUPAC Name

2-aminopent-4-ynoic acid

Traditional Name

propargylglycine

CAS Registry Number

Not Available

SMILES

NC(CC#C)C(O)=O

InChI Identifier

InChI=1S/C5H7NO2/c1-2-3-4(6)5(7)8/h1,4H,3,6H2,(H,7,8)

InChI Key

DGYHPLMPMRKMPD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Unsaturated fatty acid
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Acetylide
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Primary amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.6	ALOGPS
logP	-2.7	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.15	ChemAxon
pKa (Strongest Basic)	9.19	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	28.08 m³·mol⁻¹	ChemAxon
Polarizability	11.03 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	121.105	30932474
DeepCCS	[M-H]-	118.305	30932474
DeepCCS	[M-2H]-	154.613	30932474
DeepCCS	[M+Na]+	129.23	30932474
AllCCS	[M+H]+	128.8	32859911
AllCCS	[M+H-H2O]+	124.4	32859911
AllCCS	[M+NH4]+	132.8	32859911
AllCCS	[M+Na]+	133.9	32859911
AllCCS	[M-H]-	123.2	32859911
AllCCS	[M+Na-2H]-	126.3	32859911
AllCCS	[M+HCOO]-	129.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
DL-Propargylglycine	NC(CC#C)C(O)=O	1958.5	Standard polar	33892256
DL-Propargylglycine	NC(CC#C)C(O)=O	1010.7	Standard non polar	33892256
DL-Propargylglycine	NC(CC#C)C(O)=O	1352.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
DL-Propargylglycine,2TMS,isomer #1	C#CCC(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	1264.8	Semi standard non polar	33892256
DL-Propargylglycine,2TMS,isomer #1	C#CCC(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	1245.4	Standard non polar	33892256
DL-Propargylglycine,2TMS,isomer #1	C#CCC(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	1511.4	Standard polar	33892256
DL-Propargylglycine,2TMS,isomer #2	C#CCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1453.0	Semi standard non polar	33892256
DL-Propargylglycine,2TMS,isomer #2	C#CCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1302.9	Standard non polar	33892256
DL-Propargylglycine,2TMS,isomer #2	C#CCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1715.9	Standard polar	33892256
DL-Propargylglycine,3TMS,isomer #1	C#CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1483.1	Semi standard non polar	33892256
DL-Propargylglycine,3TMS,isomer #1	C#CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1385.9	Standard non polar	33892256
DL-Propargylglycine,3TMS,isomer #1	C#CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1494.9	Standard polar	33892256
DL-Propargylglycine,2TBDMS,isomer #1	C#CCC(N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1680.3	Semi standard non polar	33892256
DL-Propargylglycine,2TBDMS,isomer #1	C#CCC(N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1677.1	Standard non polar	33892256
DL-Propargylglycine,2TBDMS,isomer #1	C#CCC(N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1782.3	Standard polar	33892256
DL-Propargylglycine,2TBDMS,isomer #2	C#CCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1860.3	Semi standard non polar	33892256
DL-Propargylglycine,2TBDMS,isomer #2	C#CCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1732.8	Standard non polar	33892256
DL-Propargylglycine,2TBDMS,isomer #2	C#CCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1874.5	Standard polar	33892256
DL-Propargylglycine,3TBDMS,isomer #1	C#CCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2115.8	Semi standard non polar	33892256
DL-Propargylglycine,3TBDMS,isomer #1	C#CCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2018.7	Standard non polar	33892256
DL-Propargylglycine,3TBDMS,isomer #1	C#CCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1851.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - DL-Propargylglycine GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-9000000000-80cc83587065e9b6315d	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - DL-Propargylglycine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - DL-Propargylglycine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - DL-Propargylglycine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - DL-Propargylglycine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - DL-Propargylglycine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - DL-Propargylglycine 10V, Positive-QTOF	splash10-014i-9000000000-154314b04b61a40a4998	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - DL-Propargylglycine 20V, Positive-QTOF	splash10-0gbc-9000000000-4b6a1541b24abed61d21	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - DL-Propargylglycine 40V, Positive-QTOF	splash10-0uy0-9000000000-2075961122c6dab771bc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - DL-Propargylglycine 10V, Negative-QTOF	splash10-03dj-9800000000-fefbf9690b1ed4cd91aa	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - DL-Propargylglycine 20V, Negative-QTOF	splash10-03dj-9500000000-9f3ce2358cf0c2f79a2d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - DL-Propargylglycine 40V, Negative-QTOF	splash10-0f6x-9000000000-f04f90e6540b20ac364b	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

86268

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for DL-Propargylglycine (HMDB0251529)

MOL for HMDB0251529 (DL-Propargylglycine)

3D MOL for HMDB0251529 (DL-Propargylglycine)

3D SDF for HMDB0251529 (DL-Propargylglycine)

3D-SDF for HMDB0251529 (DL-Propargylglycine)

PDB for HMDB0251529 (DL-Propargylglycine)

3D PDB for HMDB0251529 (DL-Propargylglycine)

SMILES for HMDB0251529 (DL-Propargylglycine)

INCHI for HMDB0251529 (DL-Propargylglycine)

Structure for HMDB0251529 (DL-Propargylglycine)

3D Structure for HMDB0251529 (DL-Propargylglycine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra