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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2014-04-16 17:47:00 UTC

Update Date

2021-09-14 15:46:08 UTC

HMDB ID

HMDB0061678

Secondary Accession Numbers

HMDB61678

Metabolite Identification

Common Name

Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate

Description

Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate belongs to the class of organic compounds known as pyrrolidine carboxylic acids. Pyrrolidine carboxylic acids are compounds containing a pyrrolidine ring which bears a carboxylic acid. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate is a very strong basic compound (based on its pKa).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylic acid	Generator

Chemical Formula

C₇H₁₃NO₃

Average Molecular Weight

159.183

Monoisotopic Molecular Weight

159.089543287

IUPAC Name

methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate

Traditional Name

methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1CNC(CO)C1

InChI Identifier

InChI=1S/C7H13NO3/c1-11-7(10)5-2-6(4-9)8-3-5/h5-6,8-9H,2-4H2,1H3

InChI Key

BSILTUUPJBINLI-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolidine carboxylic acids. Pyrrolidine carboxylic acids are compounds containing a pyrrolidine ring which bears a carboxylic acid. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolidines

Sub Class

Pyrrolidine carboxylic acids and derivatives

Direct Parent

Pyrrolidine carboxylic acids

Alternative Parents

Substituents

Pyrrolidine carboxylic acid
Methyl ester
1,2-aminoalcohol
Amino acid or derivatives
Carboxylic acid ester
Carboxylic acid derivative
Secondary aliphatic amine
Azacycle
Secondary amine
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

secondary amino compound (CHEBI:70830 )
pyrrolidines (CHEBI:70830 )
primary alcohol (CHEBI:70830 )
methyl ester (CHEBI:70830 )
beta-amino acid ester (CHEBI:70830 )

Ontology

Not Available

Exogenous (HMDB: HMDB0061678)

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
Water Solubility	59.3 g/L	ALOGPS
logP	-0.91	ALOGPS
logP	-0.89	ChemAxon
logS	-0.43	ALOGPS
pKa (Strongest Acidic)	15.12	ChemAxon
pKa (Strongest Basic)	9.66	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.56 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	39.05 m³·mol⁻¹	ChemAxon
Polarizability	16.53 Å³	ChemAxon
Number of Rings	1	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
DarkChem	[M+H]+	135.756	31661259
DarkChem	[M-H]-	134.077	31661259
DeepCCS	[M+H]+	142.273	30932474
DeepCCS	[M-H]-	139.32	30932474
DeepCCS	[M-2H]-	175.845	30932474
DeepCCS	[M+Na]+	151.262	30932474
AllCCS	[M+H]+	135.5	32859911
AllCCS	[M+H-H2O]+	131.2	32859911
AllCCS	[M+NH4]+	139.5	32859911
AllCCS	[M+Na]+	140.6	32859911
AllCCS	[M-H]-	134.9	32859911
AllCCS	[M+Na-2H]-	136.4	32859911
AllCCS	[M+HCOO]-	138.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate	COC(=O)C1CNC(CO)C1	2416.7	Standard polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate	COC(=O)C1CNC(CO)C1	1274.2	Standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate	COC(=O)C1CNC(CO)C1	1529.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TMS,isomer #1	COC(=O)C1CNC(CO[Si](C)(C)C)C1	1431.3	Semi standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TMS,isomer #2	COC(=O)C1CC(CO)N([Si](C)(C)C)C1	1404.2	Semi standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TMS,isomer #1	COC(=O)C1CC(CO[Si](C)(C)C)N([Si](C)(C)C)C1	1508.8	Semi standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TMS,isomer #1	COC(=O)C1CC(CO[Si](C)(C)C)N([Si](C)(C)C)C1	1617.5	Standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TMS,isomer #1	COC(=O)C1CC(CO[Si](C)(C)C)N([Si](C)(C)C)C1	1810.6	Standard polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TBDMS,isomer #1	COC(=O)C1CNC(CO[Si](C)(C)C(C)(C)C)C1	1656.4	Semi standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TBDMS,isomer #2	COC(=O)C1CC(CO)N([Si](C)(C)C(C)(C)C)C1	1667.9	Semi standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TBDMS,isomer #1	COC(=O)C1CC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1	1967.9	Semi standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TBDMS,isomer #1	COC(=O)C1CC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1	2057.8	Standard non polar	33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TBDMS,isomer #1	COC(=O)C1CC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C1	2090.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9600000000-69d890687161ad9def59	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate GC-MS (1 TMS) - 70eV, Positive	splash10-00di-8920000000-56034396b231d086c62a	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Positive-QTOF	splash10-03dl-0900000000-efc97cb364cbf5cd4b22	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Positive-QTOF	splash10-01ox-4900000000-3156d2dae796c801d681	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Positive-QTOF	splash10-00lr-9100000000-c132980dfeda8abacdc1	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Negative-QTOF	splash10-0a4i-0900000000-cc9ec320ff04d451536b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Negative-QTOF	splash10-0a6u-3900000000-5e2730043cbaabc70135	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Negative-QTOF	splash10-00xr-9000000000-5f68b648ba1ad99f8229	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Negative-QTOF	splash10-0a6s-5900000000-64c39f96272a15e5614a	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Negative-QTOF	splash10-014m-9000000000-e29888f8177dc776cf76	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Negative-QTOF	splash10-052f-9300000000-f41e5d8a4303fa1625f7	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Positive-QTOF	splash10-03di-0900000000-f565ed88f7b8e5cfc485	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Positive-QTOF	splash10-0f89-9400000000-fdf2c1f22481ad817130	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Positive-QTOF	splash10-015c-9000000000-1f3fa0eb163d73d40f03	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23129459

PDB ID

Not Available

ChEBI ID

70830

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

Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]

Showing metabocard for Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate (HMDB0061678)

MOL for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

3D MOL for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

3D SDF for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

3D-SDF for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

PDB for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

3D PDB for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

SMILES for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

INCHI for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

Structure for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

3D Structure for HMDB0061678 (Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra