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Showing NP-Card for 4-hydroxy-1,5-dimethylpyrimidin-2-one (NP0324991)

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Record Information
Version2.0
Created at2022-09-12 05:24:42 UTC
Updated at2022-09-12 05:24:42 UTC
NP-MRD IDNP0324991
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-hydroxy-1,5-dimethylpyrimidin-2-one
Description1,5-Dimethyluracil, also known as 1-methylthymine, 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. 1,5-Dimethyluracil is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. 4-hydroxy-1,5-dimethylpyrimidin-2-one is found in Trypanosoma brucei. 4-hydroxy-1,5-dimethylpyrimidin-2-one was first documented in 1978 (PMID: 27260). Based on a literature review a small amount of articles have been published on 1,5-dimethyluracil (PMID: 623867) (PMID: 19670894) (PMID: 21472961).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)


  Mrv1652309122207242D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    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
    2.1434   -0.4125    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
    0.7145   -1.2375    0.0000 O   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3154   -0.8608    0.0509 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0145   -0.1742    0.0339 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1984   -0.7909    0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3558   -0.0847    0.2091 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5930   -0.7957    0.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3414    1.2446   -0.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4533    1.8434   -0.0444 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1791    1.8686   -0.2321 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9870    1.1896   -0.2057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1960    1.8756   -0.4247 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7729   -0.8410   -0.9817 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0341   -0.2835    0.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2761   -1.8861    0.4097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1769   -1.8532    0.4276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4164   -0.0684    0.6689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9301   -1.3818   -0.4235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5465   -1.4736    1.3103 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5947    2.4719    0.2987 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2  9  1  0
  9 10  1  0
  9  8  2  0
  8  6  1  0
  6  7  2  0
  6  4  1  0
  5 15  1  0
  5 16  1  0
  5 17  1  0
  3 14  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
 10 18  1  0
M  END
Download

3D SDF for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)


  Mrv1652309122207242D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    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
    2.1434   -0.4125    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
    0.7145   -1.2375    0.0000 O   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0324991

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=C(C)C(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N2O2/c1-4-3-8(2)6(10)7-5(4)9/h3H,1-2H3,(H,7,9,10)

> <INCHI_KEY>
GKMIDMKPBOUSBQ-UHFFFAOYSA-N

> <FORMULA>
C6H8N2O2

> <MOLECULAR_WEIGHT>
140.142

> <EXACT_MASS>
140.058577506

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.554244043319546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-1,5-dimethyl-1,2-dihydropyrimidin-2-one

> <JCHEM_LOGP>
0.13143635933333356

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.78703468353759

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6101116981620884

> <JCHEM_POLAR_SURFACE_AREA>
52.900000000000006

> <JCHEM_REFRACTIVITY>
35.5448

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-1,5-dimethylpyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)

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PDB for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)
HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334   3.850   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       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)
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SMILES for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)
CN1C=C(C)C(O)=NC1=O
Download
INCHI for NP0324991 (4-hydroxy-1,5-dimethylpyrimidin-2-one)
InChI=1S/C6H8N2O2/c1-4-3-8(2)6(10)7-5(4)9/h3H,1-2H3,(H,7,9,10)
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View in JSmol
Synonyms
ValueSource
1-MethylthymineChEBI
Chemical FormulaC6H8N2O2
Average Mass140.1420 Da
Monoisotopic Mass140.05858 Da
IUPAC Name4-hydroxy-1,5-dimethyl-1,2-dihydropyrimidin-2-one
Traditional Name4-hydroxy-1,5-dimethylpyrimidin-2-one
CAS Registry NumberNot Available
SMILES
CN1C=C(C)C(O)=NC1=O
InChI Identifier
InChI=1S/C6H8N2O2/c1-4-3-8(2)6(10)7-5(4)9/h3H,1-2H3,(H,7,9,10)
InChI KeyGKMIDMKPBOUSBQ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Trypanosoma bruceiLOTUS Database
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
    • 

  • Pyrimidone
    • 

  • Hydropyrimidine
    • 

  • Heteroaromatic compound
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.13ChemAxon
pKa (Strongest Acidic)7.79ChemAxon
pKa (Strongest Basic)-2.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area52.9 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.54 m³·mol⁻¹ChemAxon
Polarizability13.55 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID86632  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound95961  
PDB IDNot Available
ChEBI ID74765  
Good Scents IDNot Available
References
General References
  1. Brabec V, Christian SD, Dryhurst G: Temperature dependence of the interfacial behavior of uracil derivatives. Biophys Chem. 1978 May;8(2):151-62. doi: 10.1016/0301-4622(78)80006-4. [PubMed:27260  ] 
  2. Brabec V, Christian SD, Dryhurst G: Potential and structure controlled interfacial behavior of uracil derivatives. Biophys Chem. 1978 Jan;7(4):253-68. doi: 10.1016/0301-4622(78)85002-9. [PubMed:623867  ] 
  3. Etinski M, Fleig T, Marian CM: Intersystem crossing and characterization of dark states in the pyrimidine nucleobases uracil, thymine, and 1-methylthymine. J Phys Chem A. 2009 Oct 29;113(43):11809-16. doi: 10.1021/jp902944a. [PubMed:19670894  ] 
  4. Kunitski M, Nosenko Y, Brutschy B: On the nature of the long-lived "dark" state of isolated 1-methylthymine. Chemphyschem. 2011 Jul 11;12(10):2024-30. doi: 10.1002/cphc.201000985. Epub 2011  Apr 5. [PubMed:21472961  ] 
  5. LOTUS database [Link]