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Showing metabocard for Dihydrothymine (HMDB0000079)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:30 UTC
HMDB IDHMDB0000079
Secondary Accession Numbers
  • HMDB00079
Metabolite Identification
Common NameDihydrothymine
DescriptionDihydrothymine (CAS: 696-04-8) 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 into 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 the 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 HMDB0000079 (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
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3D MOL for HMDB0000079 (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
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3D SDF for HMDB0000079 (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>
HMDB0000079

> <DATABASE_NAME>
hmdb

> <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

$$$$
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3D-SDF for HMDB0000079 (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
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PDB for HMDB0000079 (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 HMDB0000079 (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 HMDB0000079 (Dihydrothymine)

C[C@H]1CNC(=O)NC1=O
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INCHI for HMDB0000079 (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 JSmolView NMR AssignmentsView Stereo Labels
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 Molecular Weight128.131
Monoisotopic Molecular Weight128.058577506
IUPAC Name(5S)-5-methyl-1,3-diazinane-2,4-dione
Traditional Name(5S)-5-methyl-1,3-diazinane-2,4-dione
CAS Registry Number19140-80-8
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 KeyNBAKTGXDIBVZOO-VKHMYHEASA-N
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
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+MetCCS_train_pos131.18830932474
[M+H]+Not Available131.17http://allccs.zhulab.cn/database/detail?ID=AllCCS00000462
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Prostate
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified0.0 - 24.0 uMNot SpecifiedBothDihydropyrimidinase deficiency details
Cerebrospinal Fluid (CSF)Detected and Quantified4.0 - 5.2 uMAdult (>18 years old)Not SpecifiedBeta-ureidopropionase deficiency details
UrineDetected and Quantified11.664 +/- 5.285 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
Associated Disorders and Diseases
Disease References
Dihydropyrimidinase deficiency
  1. van Kuilenburg AB, Meijer J, Dobritzsch D, Meinsma R, Duran M, Lohkamp B, Zoetekouw L, Abeling NG, van Tinteren HL, Bosch AM: Clinical, biochemical and genetic findings in two siblings with a dihydropyrimidinase deficiency. Mol Genet Metab. 2007 Jun;91(2):157-64. Epub 2007 Mar 26. [PubMed:17383919 ]
Beta-ureidopropionase deficiency
  1. van Kuilenburg AB, Meinsma R, Beke E, Assmann B, Ribes A, Lorente I, Busch R, Mayatepek E, Abeling NG, van Cruchten A, Stroomer AE, van Lenthe H, Zoetekouw L, Kulik W, Hoffmann GF, Voit T, Wevers RA, Rutsch F, van Gennip AH: beta-Ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities. Hum Mol Genet. 2004 Nov 15;13(22):2793-801. Epub 2004 Sep 22. [PubMed:15385443 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
  • 222748 (Dihydropyrimidinase deficiency)
  • 613161 (Beta-ureidopropionase deficiency)
  • 610247 (Eosinophilic esophagitis)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021892
KNApSAcK IDNot Available
Chemspider ID589127
KEGG Compound IDC00906
BioCyc IDDIHYDRO-THYMINE
BiGG IDNot Available
Wikipedia LinkDihydrothymine
METLIN IDNot Available
PubChem Compound676414
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH ID56DTHM
MarkerDB IDMDB00000043
Good Scents IDNot Available
References
Synthesis ReferenceYamane, Tetsuo; Wyluda, Benjamin J.; Shulman, Robert G. Dihydrothymine from ultraviolet-irradiated DNA. Proceedings of the National Academy of Sciences of the United States of America (1967), 58(2), 439-42.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Dihydropyrimidinase
General function:
Involved in hydrolase activity
Specific function:
Catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Can catalyze the ring opening of 5,6-dihydrouracil to N-carbamyl-alanine and of 5,6-dihydrothymine to N-carbamyl-amino isobutyrate.
Gene Name:
DPYS
Uniprot ID:
Q14117
Molecular weight:
56629.36
Reactions
Dihydrothymine + Water → Ureidoisobutyric aciddetails
Enzyme Details
2. Dihydropyrimidine dehydrogenase [NADP(+)]
General function:
Involved in electron carrier activity
Specific function:
Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
Gene Name:
DPYD
Uniprot ID:
Q12882
Molecular weight:
111400.32
Reactions
Dihydrothymine + NADP → Thymine + NADPH + Hydrogen Iondetails