Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:11:49 UTC
Update Date2021-09-26 22:55:02 UTC
HMDB IDHMDB0246161
Secondary Accession NumbersNone
Metabolite Identification
Common Name(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate
Description(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate belongs to the class of organic compounds known as pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring. Based on a literature review very few articles have been published on (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate. This compound has been identified in human blood as reported by (PMID: 31557052 ). (s)-ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 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
Thumb
Synonyms
ValueSource
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylic acidGenerator
Chemical FormulaC20H25ClN4O4
Average Molecular Weight420.89
Monoisotopic Molecular Weight420.156433
IUPAC Nameethyl 4-{[(3-chloro-4-methoxyphenyl)methyl]amino}-2-[2-(hydroxymethyl)pyrrolidin-1-yl]pyrimidine-5-carboxylate
Traditional Nameethyl 4-{[(3-chloro-4-methoxyphenyl)methyl]amino}-2-[2-(hydroxymethyl)pyrrolidin-1-yl]pyrimidine-5-carboxylate
CAS Registry NumberNot Available
SMILES
CCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO
InChI Identifier
InChI=1S/C20H25ClN4O4/c1-3-29-19(27)15-11-23-20(25-8-4-5-14(25)12-26)24-18(15)22-10-13-6-7-17(28-2)16(21)9-13/h6-7,9,11,14,26H,3-5,8,10,12H2,1-2H3,(H,22,23,24)
InChI KeyNUTJUOHYJBWTSH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidinecarboxylic acids
Alternative Parents
Substituents
  • Pyrimidine-5-carboxylic acid
  • Phenoxy compound
  • Anisole
  • Methoxybenzene
  • Dialkylarylamine
  • Benzylamine
  • Phenol ether
  • Alkyl aryl ether
  • Aminopyrimidine
  • Chlorobenzene
  • Halobenzene
  • Aryl chloride
  • Aryl halide
  • Monocyclic benzene moiety
  • Imidolactam
  • Benzenoid
  • Heteroaromatic compound
  • Vinylogous amide
  • Pyrrolidine
  • Carboxylic acid ester
  • Ether
  • Carboxylic acid derivative
  • Azacycle
  • Organohalogen compound
  • Primary alcohol
  • Amine
  • Organic nitrogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Organochloride
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
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
logP3.12ALOGPS
logP3.86ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)14.98ChemAxon
pKa (Strongest Basic)5.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area96.81 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity113.76 m³·mol⁻¹ChemAxon
Polarizability44.52 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+195.25630932474
DeepCCS[M-H]-192.54330932474
DeepCCS[M-2H]-227.21630932474
DeepCCS[M+Na]+202.41730932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylateCCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO4668.8Standard polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylateCCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO3435.3Standard non polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylateCCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO3489.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TMS,isomer #1CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C3392.2Semi standard non polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TMS,isomer #1CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C3170.0Standard non polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TMS,isomer #1CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C4307.9Standard polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TBDMS,isomer #1CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C(C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C(C)(C)C3688.2Semi standard non polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TBDMS,isomer #1CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C(C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C(C)(C)C3585.5Standard non polar33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TBDMS,isomer #1CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C(C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C(C)(C)C4390.9Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (Non-derivatized) - 70eV, Positivesplash10-056s-3109000000-583a9b2605bc09129cee2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 10V, Positive-QTOFsplash10-00di-0103900000-a732388f735f3e1650562021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 20V, Positive-QTOFsplash10-0a6r-0709200000-d3bae7f6be4e7c3bcfe02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 40V, Positive-QTOFsplash10-056r-0903000000-425ca8eec6f3450f16602021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 10V, Negative-QTOFsplash10-014i-1014900000-c4743fea6488129dbaf02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 20V, Negative-QTOFsplash10-015a-0149200000-fd0df7943899312f65662021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 40V, Negative-QTOFsplash10-000x-6941000000-fc1e764005f368ccb3152021-10-12Wishart 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 ID11532233
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22665593
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 ]