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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-12 00:34:44 UTC
Update Date2021-09-26 23:18:27 UTC
HMDB IDHMDB0260368
Secondary Accession NumbersNone
Metabolite Identification
Common Name6-(Cyclopentylideneamino)-1H-pyrimidin-2-one
Description4-(cyclopentylideneamino)pyrimidin-2-ol belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review very few articles have been published on 4-(cyclopentylideneamino)pyrimidin-2-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 6-(cyclopentylideneamino)-1h-pyrimidin-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 6-(Cyclopentylideneamino)-1H-pyrimidin-2-one 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 FormulaC9H11N3O
Average Molecular Weight177.207
Monoisotopic Molecular Weight177.090211986
IUPAC Name6-(cyclopentylideneamino)-1,2-dihydropyrimidin-2-one
Traditional Name4-(cyclopentylideneamino)-3H-pyrimidin-2-one
CAS Registry NumberNot Available
SMILES
O=C1NC(=CC=N1)N=C1CCCC1
InChI Identifier
InChI=1S/C9H11N3O/c13-9-10-6-5-8(12-9)11-7-3-1-2-4-7/h5-6H,1-4H2,(H,10,12,13)
InChI KeyDBMDNUOEEGTTRE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Heteroaromatic compound
  • Secondary ketimine
  • Azomethine
  • Ketimine
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not 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
logP0.88ALOGPS
logP0.76ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)8.71ChemAxon
pKa (Strongest Basic)6.47ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area53.82 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity58.7 m³·mol⁻¹ChemAxon
Polarizability18.43 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
AllCCS[M+H]+140.2232859911
AllCCS[M+H-H2O]+135.89832859911
AllCCS[M+Na]+145.40832859911
AllCCS[M+NH4]+144.24732859911
AllCCS[M-H]-139.44732859911
AllCCS[M+Na-2H]-140.03232859911
AllCCS[M+HCOO]-140.74832859911
DeepCCS[M+H]+142.76830932474
DeepCCS[M-H]-140.39630932474
DeepCCS[M-2H]-175.72730932474
DeepCCS[M+Na]+150.19430932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
6-(Cyclopentylideneamino)-1H-pyrimidin-2-oneO=C1NC(=CC=N1)N=C1CCCC12589.1Standard polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-oneO=C1NC(=CC=N1)N=C1CCCC11833.7Standard non polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-oneO=C1NC(=CC=N1)N=C1CCCC11969.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
6-(Cyclopentylideneamino)-1H-pyrimidin-2-one,1TMS,isomer #1C[Si](C)(C)N1C(N=C2CCCC2)=CC=NC1=O1887.4Semi standard non polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-one,1TMS,isomer #1C[Si](C)(C)N1C(N=C2CCCC2)=CC=NC1=O1820.5Standard non polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-one,1TMS,isomer #1C[Si](C)(C)N1C(N=C2CCCC2)=CC=NC1=O2598.8Standard polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(N=C2CCCC2)=CC=NC1=O2053.1Semi standard non polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(N=C2CCCC2)=CC=NC1=O2042.3Standard non polar33892256
6-(Cyclopentylideneamino)-1H-pyrimidin-2-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(N=C2CCCC2)=CC=NC1=O2698.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 6-(Cyclopentylideneamino)-1H-pyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positivesplash10-003b-5900000000-c366b8760596d7cce5c82021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-(Cyclopentylideneamino)-1H-pyrimidin-2-one 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53751536
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 ]