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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:42:52 UTC
Update Date2021-09-26 23:06:28 UTC
HMDB IDHMDB0253320
Secondary Accession NumbersNone
Metabolite Identification
Common Name[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate
Description[3-azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate 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 a significant number of articles have been published on [3-azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate. This compound has been identified in human blood as reported by (PMID: 31557052 ). [(2s,3s,5r)-3-azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2s,3s)-2-amino-3-methylpentanoate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate 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
[3-Azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoic acidGenerator
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoic acidGenerator
Chemical FormulaC16H24N6O5
Average Molecular Weight380.405
Monoisotopic Molecular Weight380.180817897
IUPAC Name[3-azido-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate
Traditional Name[3-azido-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate
CAS Registry NumberNot Available
SMILES
CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O
InChI Identifier
InChI=1S/C16H24N6O5/c1-4-8(2)13(17)15(24)26-7-11-10(20-21-18)5-12(27-11)22-6-9(3)14(23)19-16(22)25/h6,8,10-13H,4-5,7,17H2,1-3H3,(H,19,23,25)
InChI KeyQUANSGVUESEHKX-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
  • Isoleucine or derivatives
  • Alpha-amino acid ester
  • Alpha-amino acid or derivatives
  • Fatty acid ester
  • Pyrimidone
  • Hydropyrimidine
  • Fatty acyl
  • Pyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Vinylogous amide
  • Amino acid or derivatives
  • Azo compound
  • Azo imide
  • Carboxylic acid ester
  • Lactam
  • Urea
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic zwitterion
  • Hydrocarbon derivative
  • Organic oxide
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Primary amine
  • Organonitrogen compound
  • Organooxygen compound
  • Organic salt
  • Organic oxygen 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
logP1.44ALOGPS
logP1.12ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)9.96ChemAxon
pKa (Strongest Basic)7.47ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area140.39 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity92.31 m³·mol⁻¹ChemAxon
Polarizability38.47 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]+193.70730932474
DeepCCS[M-H]-191.34930932474
DeepCCS[M-2H]-225.33730932474
DeepCCS[M+Na]+200.97230932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoateCCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O4253.3Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoateCCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O2685.6Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoateCCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O2951.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]3147.7Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]3070.0Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]4825.0Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]3116.1Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]3127.1Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]5254.4Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C3171.3Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C3195.4Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C4604.2Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]3119.7Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]3110.8Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]4575.3Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C3223.4Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C3227.1Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C4346.6Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]3370.4Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]3290.1Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]4820.3Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]3317.2Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]3340.7Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]5207.4Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3632.6Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3568.9Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C4573.6Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]3556.0Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]3509.5Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]4534.4Standard polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3860.9Semi standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3757.2Standard non polar33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C4327.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0019-9110000000-17b6389cf9971dc1631c2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart 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 ID25043410
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44284846
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 ]