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Showing NP-Card for Dihydrothymine (NP0001230)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:21:49 UTC
NP-MRD IDNP0001230
Secondary Accession NumbersNone
Natural Product Identification
Common NameDihydrothymine
DescriptionDihydrothymine is an intermediate breakdown product of thymine. Dihydropyrimidine dehydrogenase catalyzes the reduction of thymine into 5,6-dihydrothymine then dihydropyrimidinase hydrolyzes 5,6-dihydrothymine into N-carbamyl-beta-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-beta-alanine to beta-alanine. When present at abnormally high levels, dihydrothymine can be toxic, although the mechanism of toxicity is not clear. In particular, patients with dihydropyrimidinase deficiency exhibit highly increased concentrations of 5,6-dihydrouracil and 5,6-dihydrothymine, and moderately increased concentrations of uracil and thymine can be detected in urine. Dihydropyrimidinase deficiency is a disorder that can cause neurological and gastrointestinal problems in some affected individuals. The most common neurological abnormalities that occur are intellectual disability, seizures, weak muscle tone (hypotonia), abnormally small head size (microcephaly), and autistic behaviours that affect communication and social interaction. Gastrointestinal problems that occur in dihydropyrimidinase deficiency include backflow of acidic stomach contents into the esophagus (gastroesophageal reflux) and recurrent episodes of vomiting.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001230 (Dihydrothymine)


  Mrv1652305082019302D          

  9  9  0  0  0  0            999 V2000
    0.1786   -1.1344    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931   -0.7219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6077   -1.1344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931    0.1031    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1785    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1786    1.3407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359    0.1031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2504    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359   -0.7219    0.0000 C   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
  2  4  1  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  6  0  0  0
  7  9  1  0  0  0  0
  1  9  1  0  0  0  0
M  END
Download

3D MOL for NP0001230 (Dihydrothymine)

HMDB0000079
     RDKit          3D
Dihydrothymine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.6124   -0.3251   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8151    0.6099    0.2068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1905   -0.2549    1.2674 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7845   -1.1125    0.6736 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8124   -0.5551   -0.1410 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9161   -1.1238   -0.3149 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    0.7119   -0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2356    1.3209   -0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051    2.4725   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0301    0.2257   -1.5541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4311   -0.7316   -0.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9484   -1.1647   -1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5468    1.2939    0.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3114    0.4438    1.9991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788   -0.8119    1.7934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7956   -2.1620    0.8012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1988    1.1629   -1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  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
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  0
  7 17  1  0
M  END
Download

3D SDF for NP0001230 (Dihydrothymine)


  Mrv1652305082019302D          

  9  9  0  0  0  0            999 V2000
    0.1786   -1.1344    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931   -0.7219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6077   -1.1344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8931    0.1031    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1785    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1786    1.3407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359    0.1031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2504    0.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5359   -0.7219    0.0000 C   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
  2  4  1  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  6  0  0  0
  7  9  1  0  0  0  0
  1  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001230

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1CNC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)/t3-/m0/s1

> <INCHI_KEY>
NBAKTGXDIBVZOO-VKHMYHEASA-N

> <FORMULA>
C5H8N2O2

> <MOLECULAR_WEIGHT>
128.131

> <EXACT_MASS>
128.058577506

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.032355612950356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S)-5-methyl-1,3-diazinane-2,4-dione

> <ALOGPS_LOGP>
-0.80

> <JCHEM_LOGP>
-0.670221453

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.799734416362337

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.699408342323004

> <JCHEM_PKA_STRONGEST_BASIC>
-7.380677679727569

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
30.320000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.87e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-5-methyl-1,3-diazinane-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001230 (Dihydrothymine)

HMDB0000079
     RDKit          3D
Dihydrothymine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.6124   -0.3251   -0.7091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8151    0.6099    0.2068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1905   -0.2549    1.2674 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7845   -1.1125    0.6736 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8124   -0.5551   -0.1410 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9161   -1.1238   -0.3149 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    0.7119   -0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2356    1.3209   -0.5312 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051    2.4725   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0301    0.2257   -1.5541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4311   -0.7316   -0.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9484   -1.1647   -1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5468    1.2939    0.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3114    0.4438    1.9991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788   -0.8119    1.7934 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7956   -2.1620    0.8012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1988    1.1629   -1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  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
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  0
  7 17  1  0
M  END
Download

PDB for NP0001230 (Dihydrothymine)

HEADER    PROTEIN                                 08-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAY-20         0                                  
HETATM    1  N   UNK     0       0.333  -2.118   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.667  -1.347   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.001  -2.118   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       1.667   0.192   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.333   0.963   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.333   2.503   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.000   0.192   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.334   0.963   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.000  -1.347   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    1                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for NP0001230 (Dihydrothymine)

COMPND    HMDB0000079
HETATM    1  C1  UNL     1      -1.612  -0.325  -0.709  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.815   0.610   0.207  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.190  -0.255   1.267  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.784  -1.112   0.674  1.00  0.00           N  
HETATM    5  C4  UNL     1       1.812  -0.555  -0.141  1.00  0.00           C  
HETATM    6  O1  UNL     1       2.916  -1.124  -0.315  1.00  0.00           O  
HETATM    7  N2  UNL     1       1.494   0.712  -0.753  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.236   1.321  -0.531  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.005   2.472  -0.962  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.030   0.226  -1.554  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.431  -0.732  -0.074  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.948  -1.165  -1.043  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.547   1.294   0.694  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.311   0.444   1.999  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.979  -0.812   1.793  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.796  -2.162   0.801  1.00  0.00           H  
HETATM   17  H8  UNL     1       2.199   1.163  -1.353  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    8   13
CONECT    3    4   14   15
CONECT    4    5   16
CONECT    5    6    6    7
CONECT    7    8   17
CONECT    8    9    9
END
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SMILES for NP0001230 (Dihydrothymine)

C[C@H]1CNC(=O)NC1=O
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INCHI for NP0001230 (Dihydrothymine)

InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)/t3-/m0/s1
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View in JSmol
Synonyms
ValueSource
(-)-(S)-5,6-DihydrothymineHMDB
(5S)-5-Methyl-1,3-diazinane-2,4-dioneHMDB
5,6-Dihydro-5-methyluracilHMDB
5,6-DihydrothymineHMDB
5-Methyl-5,6-dihydrouracilHMDB
5-Methyldihydropyrimidine-2,4(1H,3H)-dioneHMDB
Dihydro-5-methyl-2,4(1H,3H)-pyrimidinedioneHMDB
DihydrothymineHMDB
Chemical FormulaC5H8N2O2
Average Mass128.1292 Da
Monoisotopic Mass128.05858 Da
IUPAC Name(5S)-5-methyl-1,3-diazinane-2,4-dione
Traditional Name(5S)-5-methyl-1,3-diazinane-2,4-dione
CAS Registry Number696-04-8
SMILES
CC1CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)
InChI KeyNBAKTGXDIBVZOO-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
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)Varshavi.d262021-08-08View Spectrum
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
Daphnia pulexLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Paraburkholderia phymatum-
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK 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
  • N-acyl urea
  • Pyrimidone
  • Ureide
  • 1,3-diazinane
  • Dicarboximide
  • Urea
  • Carbonic acid derivative
  • Azacycle
  • Carboxylic acid derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility18.7 g/LALOGPS
logP-0.8ALOGPS
logP-0.67ChemAxon
logS-0.84ALOGPS
pKa (Strongest Acidic)11.7ChemAxon
pKa (Strongest Basic)-7.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.32 m³·mol⁻¹ChemAxon
Polarizability12.03 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000079
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021892
KNApSAcK IDC00052265
Chemspider ID589127
KEGG Compound IDC00906
BioCyc IDDIHYDRO-THYMINE
BiGG IDNot Available
Wikipedia LinkDihydrothymine
METLIN IDNot Available
PubChem Compound676414
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Hofmann U, Schwab M, Seefried S, Marx C, Zanger UM, Eichelbaum M, Murdter TE: Sensitive method for the quantification of urinary pyrimidine metabolites in healthy adults by gas chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 5;791(1-2):371-80. [PubMed:12798197 ]
  3. Assmann B, Hoffmann GF, Wagner L, Brautigam C, Seyberth HW, Duran M, Van Kuilenburg AB, Wevers R, Van Gennip AH: Dihydropyrimidinase deficiency and congenital microvillous atrophy: coincidence or genetic relation? J Inherit Metab Dis. 1997 Sep;20(5):681-8. [PubMed:9323563 ]
  4. van Lenthe H, van Kuilenburg AB, Ito T, Bootsma AH, van Cruchten A, Wada Y, van Gennip AH: Defects in pyrimidine degradation identified by HPLC-electrospray tandem mass spectrometry of urine specimens or urine-soaked filter paper strips. Clin Chem. 2000 Dec;46(12):1916-22. [PubMed:11106323 ]
  5. Rosenbaum K, Jahnke K, Curti B, Hagen WR, Schnackerz KD, Vanoni MA: Porcine recombinant dihydropyrimidine dehydrogenase: comparison of the spectroscopic and catalytic properties of the wild-type and C671A mutant enzymes. Biochemistry. 1998 Dec 15;37(50):17598-609. [PubMed:9860876 ]
  6. Sumi S, Kidouchi K, Kondou M, Hayashi K, Dobashi K, Kouwaki M, Togari H, Wada Y: Possible prediction of adverse reactions to fluorouracil by the measurement of urinary dihydrothymine and thymine. Int J Mol Med. 1998 Oct;2(4):477-82. [PubMed:9857238 ]
  7. Van Kuilenburg AB, Van Lenthe H, Van Gennip AH: Identification and tissue-specific expression of a NADH-dependent activity of dihydropyrimidine dehydrogenase in man. Anticancer Res. 1996 Jan-Feb;16(1):389-94. [PubMed:8615641 ]
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