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Showing metabocard for Pyrimidin-2-Ol (HMDB0256975)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:36:54 UTC
Update Date2022-11-23 22:29:18 UTC
HMDB IDHMDB0256975
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyrimidin-2-Ol
Descriptionpyrimidin-2-ol, also known as 2-pyridiminol, belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached 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 pyrimidin-2-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyrimidin-2-ol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyrimidin-2-Ol 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 HMDB0256975 (Pyrimidin-2-Ol)


  Mrv1652306141620462D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   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 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
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3D MOL for HMDB0256975 (Pyrimidin-2-Ol)

HMDB0256975
     RDKit          3D
pyrimidin-2-ol
 11 11  0  0  0  0  0  0  0  0999 V2000
    2.4062   -1.1934    0.0049 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2497   -0.7138    0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1699   -1.5278   -0.0217 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0938   -1.0677   -0.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2449    0.3096   -0.0072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1217    1.1408    0.0162 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1194    0.6219    0.0202 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9461   -1.7382   -0.0452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2463    0.7150   -0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2536    2.2157    0.0314 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9611    1.2379    0.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  2  1  0
  4  8  1  0
  5  9  1  0
  6 10  1  0
  7 11  1  0
M  END
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3D SDF for HMDB0256975 (Pyrimidin-2-Ol)


  Mrv1652306141620462D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   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 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256975

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1NC=CC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C4H4N2O/c7-4-5-2-1-3-6-4/h1-3H,(H,5,6,7)

> <INCHI_KEY>
VTGOHKSTWXHQJK-UHFFFAOYSA-N

> <FORMULA>
C4H4N2O

> <MOLECULAR_WEIGHT>
96.089

> <EXACT_MASS>
96.032362757

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
8.498565198963757

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-0.6464064479999998

> <ALOGPS_LOGS>
-0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.091055474350933

> <JCHEM_PKA_STRONGEST_BASIC>
0.14543176806391833

> <JCHEM_POLAR_SURFACE_AREA>
41.46

> <JCHEM_REFRACTIVITY>
25.0788

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-pyrimidone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0256975 (Pyrimidin-2-Ol)

HMDB0256975
     RDKit          3D
pyrimidin-2-ol
 11 11  0  0  0  0  0  0  0  0999 V2000
    2.4062   -1.1934    0.0049 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2497   -0.7138    0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1699   -1.5278   -0.0217 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0938   -1.0677   -0.0268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2449    0.3096   -0.0072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1217    1.1408    0.0162 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1194    0.6219    0.0202 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9461   -1.7382   -0.0452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2463    0.7150   -0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2536    2.2157    0.0314 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9611    1.2379    0.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  2  1  0
  4  8  1  0
  5  9  1  0
  6 10  1  0
  7 11  1  0
M  END
Download

PDB for HMDB0256975 (Pyrimidin-2-Ol)

HEADER    PROTEIN                                 14-JUN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-JUN-16         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0256975 (Pyrimidin-2-Ol)

COMPND    HMDB0256975
HETATM    1  O1  UNL     1       2.406  -1.193   0.005  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.250  -0.714   0.001  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.170  -1.528  -0.022  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.094  -1.068  -0.027  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.245   0.310  -0.007  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.122   1.141   0.016  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.119   0.622   0.020  1.00  0.00           N  
HETATM    8  H1  UNL     1      -1.946  -1.738  -0.045  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.246   0.715  -0.011  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.254   2.216   0.031  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.961   1.238   0.038  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    4
CONECT    4    5    8
CONECT    5    6    6    9
CONECT    6    7   10
CONECT    7   11
END
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SMILES for HMDB0256975 (Pyrimidin-2-Ol)

O=C1NC=CC=N1
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INCHI for HMDB0256975 (Pyrimidin-2-Ol)

InChI=1S/C4H4N2O/c7-4-5-2-1-3-6-4/h1-3H,(H,5,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-HydroxypyrimidineChEBI
2-PyridiminolChEBI
PyridiminolChEBI
Chemical FormulaC4H4N2O
Average Molecular Weight96.089
Monoisotopic Molecular Weight96.032362757
IUPAC Name1,2-dihydropyrimidin-2-one
Traditional Name2-pyrimidone
CAS Registry NumberNot Available
SMILES
O=C1NC=CC=N1
InChI Identifier
InChI=1S/C4H4N2O/c7-4-5-2-1-3-6-4/h1-3H,(H,5,6,7)
InChI KeyVTGOHKSTWXHQJK-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached 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 ParentHydroxypyrimidines
Alternative Parents
Substituents
  • Hydroxypyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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-0.69ALOGPS
logP-0.65ChemAxon
logS-0.28ALOGPS
pKa (Strongest Acidic)10.09ChemAxon
pKa (Strongest Basic)0.15ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area41.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity25.08 m³·mol⁻¹ChemAxon
Polarizability8.5 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+122.29830932474
DeepCCS[M-H]-119.51630932474
DeepCCS[M-2H]-155.79530932474
DeepCCS[M+Na]+130.66230932474
AllCCS[M+H]+123.832859911
AllCCS[M+H-H2O]+118.832859911
AllCCS[M+NH4]+128.432859911
AllCCS[M+Na]+129.832859911
AllCCS[M-H]-116.532859911
AllCCS[M+Na-2H]-119.832859911
AllCCS[M+HCOO]-123.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
pyrimidin-2-olO=C1NC=CC=N11980.9Standard polar33892256
pyrimidin-2-olO=C1NC=CC=N11149.6Standard non polar33892256
pyrimidin-2-olO=C1NC=CC=N11236.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
pyrimidin-2-ol,1TMS,isomer #1C[Si](C)(C)N1C=CC=NC1=O1273.7Semi standard non polar33892256
pyrimidin-2-ol,1TMS,isomer #1C[Si](C)(C)N1C=CC=NC1=O1294.6Standard non polar33892256
pyrimidin-2-ol,1TMS,isomer #1C[Si](C)(C)N1C=CC=NC1=O1630.0Standard polar33892256
pyrimidin-2-ol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC=NC1=O1475.6Semi standard non polar33892256
pyrimidin-2-ol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC=NC1=O1524.6Standard non polar33892256
pyrimidin-2-ol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=CC=NC1=O1767.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyrimidin-2-Ol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-483e9e56eb630aa0a9b92021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyrimidin-2-Ol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H 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 NMR13C NMR Spectrum (1D, 200 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 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 NMR13C NMR Spectrum (1D, 400 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, 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 NMR1H NMR Spectrum (1D, 600 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, 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 NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H 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 ID61686
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID53577
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 ]