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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:47:10 UTC
Update Date2021-09-26 23:13:15 UTC
HMDB IDHMDB0257101
Secondary Accession NumbersNone
Metabolite Identification
Common NameRaluridine
Description5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Based on a literature review very few articles have been published on 5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Raluridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Raluridine 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
SynonymsNot Available
Chemical FormulaC9H10ClFN2O4
Average Molecular Weight264.64
Monoisotopic Molecular Weight264.0313127
IUPAC Name5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5-chloro-1-[4-fluoro-5-(hydroxymethyl)oxolan-2-yl]-3H-pyrimidine-2,4-dione
CAS Registry NumberNot Available
SMILES
OCC1OC(CC1F)N1C=C(Cl)C(=O)NC1=O
InChI Identifier
InChI=1S/C9H10ClFN2O4/c10-4-2-13(9(16)12-8(4)15)7-1-5(11)6(3-14)17-7/h2,5-7,14H,1,3H2,(H,12,15,16)
InChI KeyWKVDSZYIGHLONN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2',3'-dideoxyribonucleosides
Direct ParentPyrimidine 2',3'-dideoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2',3'-dideoxyribonucleoside
  • Halopyrimidine
  • Pyrimidone
  • Aryl chloride
  • Aryl halide
  • Hydropyrimidine
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Urea
  • Lactam
  • Azacycle
  • Organoheterocyclic compound
  • Oxacycle
  • Organic oxide
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organofluoride
  • Organochloride
  • Organohalogen compound
  • Organic oxygen compound
  • Alkyl halide
  • Organic nitrogen compound
  • Alkyl fluoride
  • Alcohol
  • Organopnictogen compound
  • Hydrocarbon derivative
  • 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
logP-0.18ALOGPS
logP0.037ChemAxon
logS-0.94ALOGPS
pKa (Strongest Acidic)8.42ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area78.87 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity54.15 m³·mol⁻¹ChemAxon
Polarizability22.55 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+149.00630932474
DeepCCS[M-H]-146.64830932474
DeepCCS[M-2H]-181.51530932474
DeepCCS[M+Na]+156.5130932474
AllCCS[M+H]+155.632859911
AllCCS[M+H-H2O]+151.932859911
AllCCS[M+NH4]+159.032859911
AllCCS[M+Na]+160.032859911
AllCCS[M-H]-153.132859911
AllCCS[M+Na-2H]-153.132859911
AllCCS[M+HCOO]-153.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
RaluridineOCC1OC(CC1F)N1C=C(Cl)C(=O)NC1=O2992.8Standard polar33892256
RaluridineOCC1OC(CC1F)N1C=C(Cl)C(=O)NC1=O2303.4Standard non polar33892256
RaluridineOCC1OC(CC1F)N1C=C(Cl)C(=O)NC1=O2282.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Raluridine,2TMS,isomer #1C[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C)C2=O)CC1F2239.4Semi standard non polar33892256
Raluridine,2TMS,isomer #1C[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C)C2=O)CC1F2310.4Standard non polar33892256
Raluridine,2TMS,isomer #1C[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C)C2=O)CC1F2456.9Standard polar33892256
Raluridine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1F2712.4Semi standard non polar33892256
Raluridine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1F2745.2Standard non polar33892256
Raluridine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1F2679.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Raluridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-055e-9340000000-2cf63dabfe825d5a4fd72021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Raluridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Raluridine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Raluridine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Raluridine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Raluridine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart 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 NMR1H NMR Spectrum (1D, 200 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, 300 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, 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 NMR13C NMR Spectrum (1D, 800 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 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 ID54713
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound60708
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 ]