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Showing NP-Card for 1,3-Dimethyluracil (NP0001480)

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Record Information
Version2.0
Created at2006-05-22 14:17:38 UTC
Updated at2021-10-07 20:40:41 UTC
NP-MRD IDNP0001480
Secondary Accession NumbersNone
Natural Product Identification
Common Name1,3-Dimethyluracil
Description1,3-Dimethyluracil is a methyl derivative of uric acid, found occasionally in human urine. 1,3-Dimethyluracil is one of the purine component in urinary calculi. Methylated purines originate from the metabolism of methylxanthines (caffeine, theophylline and theobromine). Methyluric acids are indistinguishable from uric acid by simple methods routinely used in clinical laboratories, requiring the use of high-performance liquid chromatography (HPLC). Purine derivatives in urinary calculi could be considered markers of abnormal purine metabolism. The content of a purine derivative in stone depends on its average urinary excretion in the general population, similarity to the chemical structure of uric acid, and content of the latter in stone. This suggests that purines in stones represent a solid solution with uric acid as solvent. It is also plausible that methylxanthines, ubiquitous components of the diet and drugs, are involved in the pathogenesis of urolithiasis. (PMID: 11712316 , 15833286 , 3506820 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001480 (1,3-Dimethyluracil)


  Mrv1652305261923522D          

 10 10  0  0  0  0            999 V2000
   16.3074   -5.1012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1654   -5.1012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365   -5.1012    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0220   -3.8638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0220   -4.6888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4509   -4.6888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365   -3.4513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4509   -3.8638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365   -5.9262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3074   -3.4513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  2  0  0  0  0
  2  6  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  9  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  4 10  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
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3D MOL for NP0001480 (1,3-Dimethyluracil)

HMDB0002144
     RDKit          3D
1,3-Dimethyluracil
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.4456   -0.7291    0.2017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1673   -0.0151    0.1317 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1196    1.3015    0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1084    1.9368    0.2136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2345    1.1748   -0.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3461    1.7583   -0.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1567   -0.1424   -0.1701 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3189   -0.9857   -0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0474   -0.7313   -0.0939 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1286   -1.9975   -0.2390 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3595   -1.6206   -0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5488   -1.0344    1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2629   -0.0549   -0.0671 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0303    1.8391    0.4650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1520    3.0165    0.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0817   -2.0413   -0.1042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1567   -0.6416    0.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5551   -1.0332   -1.4980 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
  7  9  1  0
  9 10  2  0
  9  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
M  END
Download

3D SDF for NP0001480 (1,3-Dimethyluracil)


  Mrv1652305261923522D          

 10 10  0  0  0  0            999 V2000
   16.3074   -5.1012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1654   -5.1012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365   -5.1012    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0220   -3.8638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0220   -4.6888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4509   -4.6888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365   -3.4513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4509   -3.8638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365   -5.9262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3074   -3.4513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  2  0  0  0  0
  2  6  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  9  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  4 10  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001480

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=CC(=O)N(C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N2O2/c1-7-4-3-5(9)8(2)6(7)10/h3-4H,1-2H3

> <INCHI_KEY>
JSDBKAHWADVXFU-UHFFFAOYSA-N

> <FORMULA>
C6H8N2O2

> <MOLECULAR_WEIGHT>
140.1399

> <EXACT_MASS>
140.05857751

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.446757625263496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-0.40793886866666684

> <ALOGPS_LOGS>
0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.914477882620596

> <JCHEM_POLAR_SURFACE_AREA>
40.620000000000005

> <JCHEM_REFRACTIVITY>
35.762699999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-dimethyluracil

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001480 (1,3-Dimethyluracil)

HMDB0002144
     RDKit          3D
1,3-Dimethyluracil
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.4456   -0.7291    0.2017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1673   -0.0151    0.1317 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1196    1.3015    0.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1084    1.9368    0.2136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2345    1.1748   -0.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3461    1.7583   -0.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1567   -0.1424   -0.1701 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3189   -0.9857   -0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0474   -0.7313   -0.0939 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1286   -1.9975   -0.2390 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3595   -1.6206   -0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5488   -1.0344    1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2629   -0.0549   -0.0671 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0303    1.8391    0.4650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1520    3.0165    0.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0817   -2.0413   -0.1042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1567   -0.6416    0.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5551   -1.0332   -1.4980 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
  7  9  1  0
  9 10  2  0
  9  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
M  END
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PDB for NP0001480 (1,3-Dimethyluracil)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      30.440  -9.522   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      35.775  -9.522   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      33.108  -9.522   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      31.774  -7.212   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      31.774  -8.752   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      34.442  -8.752   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      33.108  -6.442   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      34.442  -7.212   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      33.108 -11.062   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.440  -6.442   0.000  0.00  0.00           C+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    5    6    9                                                  
CONECT    4    5    7   10                                                  
CONECT    5    1    3    4                                                  
CONECT    6    2    3    8                                                  
CONECT    7    4    8                                                       
CONECT    8    6    7                                                       
CONECT    9    3                                                            
CONECT   10    4                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for NP0001480 (1,3-Dimethyluracil)

COMPND    HMDB0002144
HETATM    1  C1  UNL     1       2.446  -0.729   0.202  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.167  -0.015   0.132  1.00  0.00           N  
HETATM    3  C2  UNL     1       1.120   1.301   0.287  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.108   1.937   0.214  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.234   1.175  -0.018  1.00  0.00           C  
HETATM    6  O1  UNL     1      -2.346   1.758  -0.084  1.00  0.00           O  
HETATM    7  N2  UNL     1      -1.157  -0.142  -0.170  1.00  0.00           N  
HETATM    8  C5  UNL     1      -2.319  -0.986  -0.417  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.047  -0.731  -0.094  1.00  0.00           C  
HETATM   10  O2  UNL     1       0.129  -1.997  -0.239  1.00  0.00           O  
HETATM   11  H1  UNL     1       2.360  -1.621  -0.431  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.549  -1.034   1.280  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.263  -0.055  -0.067  1.00  0.00           H  
HETATM   14  H4  UNL     1       2.030   1.839   0.465  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.152   3.017   0.340  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.082  -2.041  -0.104  1.00  0.00           H  
HETATM   17  H7  UNL     1      -3.157  -0.642   0.203  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.555  -1.033  -1.498  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    9
CONECT    3    4    4   14
CONECT    4    5   15
CONECT    5    6    6    7
CONECT    7    8    9
CONECT    8   16   17   18
CONECT    9   10   10
END
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SMILES for NP0001480 (1,3-Dimethyluracil)

CN1C=CC(=O)N(C)C1=O
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INCHI for NP0001480 (1,3-Dimethyluracil)

InChI=1S/C6H8N2O2/c1-7-4-3-5(9)8(2)6(7)10/h3-4H,1-2H3
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View in JSmol
Synonyms
ValueSource
2,4-Dihydroxy-1,3-dimethylpyrimidineChEBI
N,N'-dimethyluracilChEBI
N1,N3-DimethyluracilChEBI
1, 3-Dimethyl-2,4(1H,3H)-pyrimidinedioneHMDB
1,3-Dimethyl-2,4(1H,3H)-pyrimidinedioneHMDB
Chemical FormulaC6H8N2O2
Average Mass140.1399 Da
Monoisotopic Mass140.05858 Da
IUPAC Name1,3-dimethyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1,3-dimethyluracil
CAS Registry Number874-14-6
SMILES
CN1C=CC(=O)N(C)C1=O
InChI Identifier
InChI=1S/C6H8N2O2/c1-7-4-3-5(9)8(2)6(7)10/h3-4H,1-2H3
InChI KeyJSDBKAHWADVXFU-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Trypanosoma bruceiLOTUS 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
StateSolid
Experimental Properties
PropertyValueReference
Melting Point120 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-0.54Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility270 g/LALOGPS
logP-0.81ALOGPS
logP-0.41ChemAxon
logS0.28ALOGPS
pKa (Strongest Basic)-4.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.62 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.76 m³·mol⁻¹ChemAxon
Polarizability13.45 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002144
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022866
KNApSAcK IDNot Available
Chemspider ID63310
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound70122
PDB IDNot Available
ChEBI ID74763
Good Scents IDNot Available
References
General References
  1. Vartanova AE, Levina II, Rybakov VB, Ivanova OA, Trushkov IV: Donor-Acceptor Cyclopropane Ring Opening with 6-Amino-1,3-dimethyluracil and Its Use in Pyrimido[4,5-b]azepines Synthesis. J Org Chem. 2021 Sep 3;86(17):12300-12308. doi: 10.1021/acs.joc.1c01064. Epub 2021 Aug 12. [PubMed:34382810 ]
  2. Dahi-Azar S, Abdolmohammadi S, Mokhtari J: Ethanol-Drop Grinding Approach: Cadmium Oxide Nanoparticles Catalyzed the Synthesis of [1,3]Dioxolo[g][1]benzopyran-6-carboxylic Acids and Pyrido[d]pyrimidine-7-carboxylic Acids. Comb Chem High Throughput Screen. 2021;24(1):139-147. doi: 10.2174/1386207323666200712145041. [PubMed:32652906 ]