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Showing NP-Card for 4-hydroxy-1-methylpyrimidin-2-one (NP0241738)

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Record Information
Version2.0
Created at2022-09-07 01:53:38 UTC
Updated at2022-09-07 01:53:38 UTC
NP-MRD IDNP0241738
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-hydroxy-1-methylpyrimidin-2-one
Description1-Methyluracil 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. 1-Methyluracil is an extremely weak basic (essentially neutral) compound (based on its pKa). 4-hydroxy-1-methylpyrimidin-2-one is found in Alangium salviifolium and Ophiocordyceps sinensis. 4-hydroxy-1-methylpyrimidin-2-one was first documented in 1975 (PMID: 1210140). A pyrimidone that is uracil with a methyl group substituent at position 1 (PMID: 12903356) (PMID: 19058265) (PMID: 2619960).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)


  Mrv0541 04121520452D          

  9  9  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 N   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 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  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
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3D MOL for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)

     RDKit          3D

 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1696    0.0784   -0.1000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7068    0.0637   -0.0334 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0144    1.1983    0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4001    1.1137    0.0907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0452   -0.1047    0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3009   -0.1407    0.1450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2883   -1.2137    0.0246 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0659   -1.0983   -0.0344 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7467   -2.1667   -0.0936 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5145   -0.5698   -0.9079 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6080   -0.3452    0.8472 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4914    1.1413   -0.2509 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5058    2.1588    0.0307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0005    2.0314    0.1423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7592   -2.1464    0.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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3D SDF for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)


  Mrv0541 04121520452D          

  9  9  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 N   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 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  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0241738

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O2/c1-7-3-2-4(8)6-5(7)9/h2-3H,1H3,(H,6,8,9)

> <INCHI_KEY>
XBCXJKGHPABGSD-UHFFFAOYSA-N

> <FORMULA>
C5H6N2O2

> <MOLECULAR_WEIGHT>
126.115

> <EXACT_MASS>
126.042927441

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.418903827505668

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-0.85

> <JCHEM_LOGP>
-0.6316149343333334

> <ALOGPS_LOGS>
-0.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.769241363286527

> <JCHEM_PKA_STRONGEST_BASIC>
-5.266331463064229

> <JCHEM_POLAR_SURFACE_AREA>
49.410000000000004

> <JCHEM_REFRACTIVITY>
30.866000000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyluracil

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)

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PDB for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)
HEADER    PROTEIN                                 12-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-APR-15         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+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  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)
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SMILES for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)
CN1C=CC(=O)NC1=O
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INCHI for NP0241738 (4-hydroxy-1-methylpyrimidin-2-one)
InChI=1S/C5H6N2O2/c1-7-3-2-4(8)6-5(7)9/h2-3H,1H3,(H,6,8,9)
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View in JSmol
Synonyms
ValueSource
1-Methyluracil monohydrobromideMeSH
1-Methyluracil, ion (1-)MeSH
Chemical FormulaC5H6N2O2
Average Mass126.1150 Da
Monoisotopic Mass126.04293 Da
IUPAC Name1-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1-methyluracil
CAS Registry NumberNot Available
SMILES
CN1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C5H6N2O2/c1-7-3-2-4(8)6-5(7)9/h2-3H,1H3,(H,6,8,9)
InChI KeyXBCXJKGHPABGSD-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
Alangium salviifoliumLOTUS Database
Ophiocordyceps sinensisLOTUS Database
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
    • 

  • Vinylogous amide
    • 

  • Urea
    • 

  • Lactam
    • 

  • 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
logP-0.85ALOGPS
logP-0.63ChemAxon
logS-0.04ALOGPS
pKa (Strongest Acidic)8.77ChemAxon
pKa (Strongest Basic)-5.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.41 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.87 m³·mol⁻¹ChemAxon
Polarizability11.42 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12009  
PDB IDNot Available
ChEBI ID69445  
Good Scents IDNot Available
References
General References
  1. Kolosov AI: [The antiblastomatous activity of 9-methyladenine, 1-methyluracil and 1-methylthymine]. Vopr Onkol. 1975;21(5):116-7. [PubMed:1210140  ] 
  2. Kawahara S, Taira K, Sekine M, Uchimaru T: Evaluation of the hydrogen bond energy of base pairs formed between substituted 9-methyladenine derivatives and 1-methyluracil by use of molecular orbital theory. Nucleic Acids Symp Ser. 2000;(44):237-8. doi: 10.1093/nass/44.1.237. [PubMed:12903356  ] 
  3. van der Wijst T, Fonseca Guerra C, Swart M, Bickelhaupt FM, Lippert B: Rare tautomers of 1-methyluracil and 1-methylthymine: tuning relative stabilities through coordination to PtII complexes. Chemistry. 2009;15(1):209-18. doi: 10.1002/chem.200801476. [PubMed:19058265  ] 
  4. McMullan RK, Craven BM: Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K. Acta Crystallogr B. 1989 Jun 1;45 ( Pt 3):270-6. doi: 10.1107/s0108768189000777. [PubMed:2619960  ] 
  5. LOTUS database [Link]