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Showing metabocard for Thymine (HMDB0000262)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:40 UTC
HMDB IDHMDB0000262
Secondary Accession Numbers
  • HMDB00262
Metabolite Identification
Common NameThymine
DescriptionThymine, also known as 5-methyluracil, 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. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calves' thymus glands, hence its name. Thymine is one of the 4 nuelcoebases found in DNA and is essential to all life. Thymine exists in all living species, ranging from bacteria to plants to humans. Thymine combined with deoxyribose creates the nucleoside deoxythymidine (also called thymidine) which when phosphorylated to dTDP can be incorporated into DNA via DNA polymerases. Thymidine can be phosphorylated with up to three phosphoric acid groups, producing dTMP (deoxythymidine monophosphate) dTDP and/or dTTP. In RNA thymine is replaced with uracil in most cases. In DNA, thymine binds to adenine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. Within humans, thymine participates in a number of enzymatic reactions. In particular, thymine and deoxyribose 1-phosphate can be biosynthesized from thymidine through its interaction with the enzyme thymidine phosphorylase. In addition, thymine can be converted into dihydrothymine; which is mediated by the enzyme dihydropyrimidine dehydrogenase [NADP(+)].
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000262 (Thymine)

  Mrv1652309191922122D          

  9  9  0  0  0  0            999 V2000
    2.1434    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    0.7145    2.0625    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
  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 HMDB0000262 (Thymine)

HMDB0000262
     RDKit          3D
Thymine
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1857   -0.1429    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6847   -0.0612    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0879   -1.1958    0.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4245   -1.0978   -0.0309 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0276    0.1023   -0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2770    0.1910   -0.1834 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737    1.2157   -0.1282 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0673    1.1679   -0.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7712    2.2093   -0.0695 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6199   -0.3949   -0.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5008   -0.8698    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414    0.8597    0.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4203   -2.1670    0.1112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9813   -1.9832   -0.0190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7193    2.1669   -0.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0000262 (Thymine)

  Mrv1652309191922122D          

  9  9  0  0  0  0            999 V2000
    2.1434    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    0.7145    2.0625    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
  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>
HMDB0000262

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CNC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)

> <INCHI_KEY>
RWQNBRDOKXIBIV-UHFFFAOYSA-N

> <FORMULA>
C5H6N2O2

> <MOLECULAR_WEIGHT>
126.1133

> <EXACT_MASS>
126.042927446

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.422204494643946

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-0.45974051066666644

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.002512971014774

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.057944384019686

> <JCHEM_PKA_STRONGEST_BASIC>
-4.998777587344984

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
30.326400000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thymine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000262 (Thymine)

HMDB0000262
     RDKit          3D
Thymine
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1857   -0.1429    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6847   -0.0612    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0879   -1.1958    0.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4245   -1.0978   -0.0309 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0276    0.1023   -0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2770    0.1910   -0.1834 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737    1.2157   -0.1282 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0673    1.1679   -0.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7712    2.2093   -0.0695 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6199   -0.3949   -0.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5008   -0.8698    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414    0.8597    0.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4203   -2.1670    0.1112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9813   -1.9832   -0.0190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7193    2.1669   -0.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0000262 (Thymine)

HEADER    PROTEIN                                 19-SEP-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-SEP-19         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334   3.850   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 HMDB0000262 (Thymine)

COMPND    HMDB0000262
HETATM    1  C1  UNL     1       2.186  -0.143   0.109  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.685  -0.061   0.029  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.088  -1.196   0.041  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.424  -1.098  -0.031  1.00  0.00           N  
HETATM    5  C4  UNL     1      -2.028   0.102  -0.116  1.00  0.00           C  
HETATM    6  O1  UNL     1      -3.277   0.191  -0.183  1.00  0.00           O  
HETATM    7  N2  UNL     1      -1.274   1.216  -0.128  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.067   1.168  -0.058  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.771   2.209  -0.069  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.620  -0.395  -0.860  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.501  -0.870   0.892  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.541   0.860   0.476  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.420  -2.167   0.111  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.981  -1.983  -0.019  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.719   2.167  -0.194  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    3    8
CONECT    3    4   13
CONECT    4    5   14
CONECT    5    6    6    7
CONECT    7    8   15
CONECT    8    9    9
END
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SMILES for HMDB0000262 (Thymine)

CC1=CNC(=O)NC1=O
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INCHI for HMDB0000262 (Thymine)

InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,4-Dihydroxy-5-methylpyrimidineChEBI
5-Methyl-2,4(1H,3H)-pyrimidinedioneChEBI
5-Methylpyrimidine-2,4(1H,3H)-dioneChEBI
5-MethyluracilChEBI
TChEBI
ThyChEBI
ThyminChEBI
4-Hydroxy-5-methylpyrimidin-2(1H)-oneHMDB
5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dioneHMDB
5-Methyl-2,4-dihydroxypyrimidineHMDB
5-Methylpyrimidine-2,4-dioneHMDB
5 MethyluracilHMDB
Chemical FormulaC5H6N2O2
Average Molecular Weight126.1133
Monoisotopic Molecular Weight126.042927446
IUPAC Name5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymine
CAS Registry Number65-71-4
SMILES
CC1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
InChI KeyRWQNBRDOKXIBIV-UHFFFAOYSA-N
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
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point320 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.82 mg/mLYALKOWSKY,SH & DANNENFELSER,RM (1992)
LogP-0.62HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker122.42130932474
[M-H]-MetCCS_train_neg117.39330932474
[M+H]+Astarita_pos115.030932474
[M+H]+Baker126.14130932474
[M+H]+MetCCS_test_pos121.92530932474
[M-H]-Not Available119.1http://allccs.zhulab.cn/database/detail?ID=AllCCS00000320
[M+H]+Not Available123.0http://allccs.zhulab.cn/database/detail?ID=AllCCS00000320
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Placenta
  • Prostate
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Thymidine treatment
  1. Leyva A, Schornagel JH, Kraal I, Wadman SK, Pinedo HM: Clinical and biochemical studies of high-dose thymidine treatment in patients with solid tumors. J Cancer Res Clin Oncol. 1984;107(3):211-6. [PubMed:6736109 ]
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 ]
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Temporomandibular joint disorder
  1. (). Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles. . .
Periodontal Probing Depth
  1. Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Dihydropyrimidine dehydrogenase deficiency
  1. Brockstedt M, Jakobs C, Smit LM, van Gennip AH, Berger R: A new case of dihydropyrimidine dehydrogenase deficiency. J Inherit Metab Dis. 1990;13(1):121-4. [PubMed:2109146 ]
  2. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Associated OMIM IDs
  • 613161 (Beta-ureidopropionase deficiency)
  • 114500 (Colorectal cancer)
  • 274270 (Dihydropyrimidine dehydrogenase deficiency)
DrugBank IDDB03462
Phenol Explorer Compound IDNot Available
FooDB IDFDB021922
KNApSAcK IDC00001511
Chemspider ID1103
KEGG Compound IDC00178
BioCyc IDTHYMINE
BiGG ID34151
Wikipedia LinkThymine
METLIN ID290
PubChem Compound1135
PDB IDNot Available
ChEBI ID17821
Food Biomarker OntologyNot Available
VMH IDTHYM
MarkerDB IDMDB00000127
Good Scents IDNot Available
References
Synthesis ReferenceZhang, Shi-Ying; Wu, Da-Jun; Zhang, Yan-Ping. Synthesis of thymine. Zhongguo Yiyao Gongye Zazhi (1999), 30(7), 325.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. 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
Enzyme Details
2. Thymidine phosphorylase
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Reactions
Thymidine + Phosphate → Thymine + Deoxyribose 1-phosphatedetails