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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2014-04-16 17:47:00 UTC
Update Date2021-09-14 15:46:08 UTC
HMDB IDHMDB0061678
Secondary Accession Numbers
  • HMDB61678
Metabolite Identification
Common NameMethyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate
DescriptionMethyl 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
Data?1563866218
Synonyms
ValueSource
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylic acidGenerator
Chemical FormulaC7H13NO3
Average Molecular Weight159.183
Monoisotopic Molecular Weight159.089543287
IUPAC Namemethyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate
Traditional Namemethyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate
CAS Registry NumberNot 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 KeyBSILTUUPJBINLI-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolidines
Sub ClassPyrrolidine carboxylic acids and derivatives
Direct ParentPyrrolidine 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 FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
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
Water Solubility59.3 g/LALOGPS
logP-0.91ALOGPS
logP-0.89ChemAxon
logS-0.43ALOGPS
pKa (Strongest Acidic)15.12ChemAxon
pKa (Strongest Basic)9.66ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.56 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity39.05 m³·mol⁻¹ChemAxon
Polarizability16.53 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+135.75631661259
DarkChem[M-H]-134.07731661259
DeepCCS[M+H]+142.27330932474
DeepCCS[M-H]-139.3230932474
DeepCCS[M-2H]-175.84530932474
DeepCCS[M+Na]+151.26230932474
AllCCS[M+H]+135.532859911
AllCCS[M+H-H2O]+131.232859911
AllCCS[M+NH4]+139.532859911
AllCCS[M+Na]+140.632859911
AllCCS[M-H]-134.932859911
AllCCS[M+Na-2H]-136.432859911
AllCCS[M+HCOO]-138.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylateCOC(=O)C1CNC(CO)C12416.7Standard polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylateCOC(=O)C1CNC(CO)C11274.2Standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylateCOC(=O)C1CNC(CO)C11529.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TMS,isomer #1COC(=O)C1CNC(CO[Si](C)(C)C)C11431.3Semi standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TMS,isomer #2COC(=O)C1CC(CO)N([Si](C)(C)C)C11404.2Semi standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TMS,isomer #1COC(=O)C1CC(CO[Si](C)(C)C)N([Si](C)(C)C)C11508.8Semi standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TMS,isomer #1COC(=O)C1CC(CO[Si](C)(C)C)N([Si](C)(C)C)C11617.5Standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TMS,isomer #1COC(=O)C1CC(CO[Si](C)(C)C)N([Si](C)(C)C)C11810.6Standard polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TBDMS,isomer #1COC(=O)C1CNC(CO[Si](C)(C)C(C)(C)C)C11656.4Semi standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,1TBDMS,isomer #2COC(=O)C1CC(CO)N([Si](C)(C)C(C)(C)C)C11667.9Semi standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TBDMS,isomer #1COC(=O)C1CC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C11967.9Semi standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TBDMS,isomer #1COC(=O)C1CC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C12057.8Standard non polar33892256
Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate,2TBDMS,isomer #1COC(=O)C1CC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C12090.9Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9600000000-69d890687161ad9def592017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate GC-MS (1 TMS) - 70eV, Positivesplash10-00di-8920000000-56034396b231d086c62a2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 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 - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Positive-QTOFsplash10-03dl-0900000000-efc97cb364cbf5cd4b222017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Positive-QTOFsplash10-01ox-4900000000-3156d2dae796c801d6812017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Positive-QTOFsplash10-00lr-9100000000-c132980dfeda8abacdc12017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Negative-QTOFsplash10-0a4i-0900000000-cc9ec320ff04d451536b2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Negative-QTOFsplash10-0a6u-3900000000-5e2730043cbaabc701352017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Negative-QTOFsplash10-00xr-9000000000-5f68b648ba1ad99f82292017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Negative-QTOFsplash10-0a6s-5900000000-64c39f96272a15e5614a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Negative-QTOFsplash10-014m-9000000000-e29888f8177dc776cf762021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Negative-QTOFsplash10-052f-9300000000-f41e5d8a4303fa1625f72021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 10V, Positive-QTOFsplash10-03di-0900000000-f565ed88f7b8e5cfc4852021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 20V, Positive-QTOFsplash10-0f89-9400000000-fdf2c1f22481ad8171302021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methyl 5-(hydroxymethyl)pyrrolidine-3-carboxylate 40V, Positive-QTOFsplash10-015c-9000000000-1f3fa0eb163d73d40f032021-09-25Wishart 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
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23129459
PDB IDNot Available
ChEBI ID70830
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. 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 ]