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Showing metabocard for 5-Fluoropyrimidine (HMDB0246796)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:48:33 UTC
Update Date2021-09-26 22:56:06 UTC
HMDB IDHMDB0246796
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Fluoropyrimidine
Description5-Fluoropyrimidine belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. 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 a significant number of articles have been published on 5-Fluoropyrimidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-fluoropyrimidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Fluoropyrimidine 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0246796 (5-Fluoropyrimidine)


  Mrv1652309112101482D          

  7  7  0  0  0  0            999 V2000
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
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3D MOL for HMDB0246796 (5-Fluoropyrimidine)

HMDB0246796
     RDKit          3D
5-Fluoropyrimidine
 10 10  0  0  0  0  0  0  0  0999 V2000
   -2.4715    0.1237    0.1245 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1026    0.0549    0.0555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3280    1.1957    0.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0144    1.1153   -0.0360 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6432   -0.0781   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8918   -1.2103   -0.0600 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4482   -1.1597    0.0073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8625    2.1493    0.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7311   -0.1262   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0678   -2.0646    0.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  3  8  1  0
  5  9  1  0
  7 10  1  0
M  END
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3D SDF for HMDB0246796 (5-Fluoropyrimidine)


  Mrv1652309112101482D          

  7  7  0  0  0  0            999 V2000
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246796

> <DATABASE_NAME>
hmdb

> <SMILES>
FC1=CN=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C4H3FN2/c5-4-1-6-3-7-2-4/h1-3H

> <INCHI_KEY>
KSPDSMOWMQFPBL-UHFFFAOYSA-N

> <FORMULA>
C4H3FN2

> <MOLECULAR_WEIGHT>
98.08

> <EXACT_MASS>
98.028026268

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
7.718629567885971

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-fluoropyrimidine

> <ALOGPS_LOGP>
-0.01

> <JCHEM_LOGP>
0.1924373923333334

> <ALOGPS_LOGS>
-0.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-0.10958305574313687

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
22.938699999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.90e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrimidine,5-fluoro

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0246796 (5-Fluoropyrimidine)

HMDB0246796
     RDKit          3D
5-Fluoropyrimidine
 10 10  0  0  0  0  0  0  0  0999 V2000
   -2.4715    0.1237    0.1245 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1026    0.0549    0.0555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3280    1.1957    0.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0144    1.1153   -0.0360 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6432   -0.0781   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8918   -1.2103   -0.0600 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4482   -1.1597    0.0073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8625    2.1493    0.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7311   -0.1262   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0678   -2.0646    0.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  3  8  1  0
  5  9  1  0
  7 10  1  0
M  END
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PDB for HMDB0246796 (5-Fluoropyrimidine)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000  -0.000   0.000  0.00  0.00           N+0
HETATM    7  F   UNK     0       1.334   3.850   0.000  0.00  0.00           F+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    2                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0246796 (5-Fluoropyrimidine)

COMPND    HMDB0246796
HETATM    1  F1  UNL     1      -2.471   0.124   0.124  1.00  0.00           F  
HETATM    2  C1  UNL     1      -1.103   0.055   0.056  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.328   1.196   0.032  1.00  0.00           C  
HETATM    4  N1  UNL     1       1.014   1.115  -0.036  1.00  0.00           N  
HETATM    5  C3  UNL     1       1.643  -0.078  -0.083  1.00  0.00           C  
HETATM    6  N2  UNL     1       0.892  -1.210  -0.060  1.00  0.00           N  
HETATM    7  C4  UNL     1      -0.448  -1.160   0.007  1.00  0.00           C  
HETATM    8  H1  UNL     1      -0.862   2.149   0.071  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.731  -0.126  -0.137  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.068  -2.065   0.026  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3    7
CONECT    3    4    8
CONECT    4    5    5
CONECT    5    6    9
CONECT    6    7    7
CONECT    7   10
END
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SMILES for HMDB0246796 (5-Fluoropyrimidine)

FC1=CN=CN=C1
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INCHI for HMDB0246796 (5-Fluoropyrimidine)

InChI=1S/C4H3FN2/c5-4-1-6-3-7-2-4/h1-3H
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC4H3FN2
Average Molecular Weight98.08
Monoisotopic Molecular Weight98.028026268
IUPAC Name5-fluoropyrimidine
Traditional Namepyrimidine,5-fluoro
CAS Registry NumberNot Available
SMILES
FC1=CN=CN=C1
InChI Identifier
InChI=1S/C4H3FN2/c5-4-1-6-3-7-2-4/h1-3H
InChI KeyKSPDSMOWMQFPBL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. 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 ParentHalopyrimidines
Alternative Parents
Substituents
  • Halopyrimidine
  • Aryl halide
  • Aryl fluoride
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organofluoride
  • Organohalogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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-0.01ALOGPS
logP0.19ChemAxon
logS-0.22ALOGPS
pKa (Strongest Basic)-0.11ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.78 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity22.94 m³·mol⁻¹ChemAxon
Polarizability7.72 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+118.16330932474
DeepCCS[M-H]-115.81630932474
DeepCCS[M-2H]-151.84930932474
DeepCCS[M+Na]+126.52730932474
AllCCS[M+H]+120.632859911
AllCCS[M+H-H2O]+115.432859911
AllCCS[M+NH4]+125.432859911
AllCCS[M+Na]+126.732859911
AllCCS[M-H]-116.132859911
AllCCS[M+Na-2H]-119.132859911
AllCCS[M+HCOO]-122.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-FluoropyrimidineFC1=CN=CN=C11228.7Standard polar33892256
5-FluoropyrimidineFC1=CN=CN=C1735.2Standard non polar33892256
5-FluoropyrimidineFC1=CN=CN=C1734.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Fluoropyrimidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-2a5d5e24234060622e7f2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Fluoropyrimidine 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 - 5-Fluoropyrimidine 10V, Positive-QTOFsplash10-0002-9000000000-57000de647c8258728fb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Fluoropyrimidine 20V, Positive-QTOFsplash10-0002-9000000000-57000de647c8258728fb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Fluoropyrimidine 40V, Positive-QTOFsplash10-0002-9000000000-57000de647c8258728fb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Fluoropyrimidine 10V, Negative-QTOFsplash10-0002-9000000000-ea4ce90a0c833b917acf2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Fluoropyrimidine 20V, Negative-QTOFsplash10-0002-9000000000-ea4ce90a0c833b917acf2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Fluoropyrimidine 40V, Negative-QTOFsplash10-0002-9000000000-ea4ce90a0c833b917acf2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID62808
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkFluoropyrimidine
METLIN IDNot Available
PubChem Compound69605
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 ]