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Showing metabocard for Thymine (HMDB0000262)

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enzymes (2) Show 2 proteins
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
Data?1676999680
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
Not AvailableNot Available
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
PropertyValueSource
Water Solubility10.8 g/LALOGPS
logP-0.99ALOGPS
logP-0.46ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)9.06ChemAxon
pKa (Strongest Basic)-5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.33 m³·mol⁻¹ChemAxon
Polarizability11.42 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+125.52231661259
DarkChem[M-H]-121.27231661259
AllCCS[M+H]+126.96232859911
AllCCS[M-H]-121.82632859911
DeepCCS[M+H]+121.76930932474
DeepCCS[M-H]-118.67730932474
DeepCCS[M-2H]-155.09130932474
DeepCCS[M+Na]+130.32630932474
AllCCS[M+H]+127.032859911
AllCCS[M+H-H2O]+122.232859911
AllCCS[M+NH4]+131.432859911
AllCCS[M+Na]+132.732859911
AllCCS[M-H]-121.832859911
AllCCS[M+Na-2H]-124.032859911
AllCCS[M+HCOO]-126.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.9 minutes32390414
Predicted by Siyang on May 30, 20228.7352 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.93 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid565.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid319.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid91.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid219.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid60.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid271.7 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid286.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)169.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid593.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid155.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid730.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid213.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid230.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate568.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA254.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water219.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ThymineCC1=CNC(=O)NC1=O2202.0Standard polar33892256
ThymineCC1=CNC(=O)NC1=O1424.6Standard non polar33892256
ThymineCC1=CNC(=O)NC1=O1610.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Thymine,1TMS,isomer #1CC1=CN([Si](C)(C)C)C(=O)[NH]C1=O1549.1Semi standard non polar33892256
Thymine,1TMS,isomer #1CC1=CN([Si](C)(C)C)C(=O)[NH]C1=O1621.7Standard non polar33892256
Thymine,1TMS,isomer #1CC1=CN([Si](C)(C)C)C(=O)[NH]C1=O1986.2Standard polar33892256
Thymine,1TMS,isomer #2CC1=C[NH]C(=O)N([Si](C)(C)C)C1=O1530.1Semi standard non polar33892256
Thymine,1TMS,isomer #2CC1=C[NH]C(=O)N([Si](C)(C)C)C1=O1566.6Standard non polar33892256
Thymine,1TMS,isomer #2CC1=C[NH]C(=O)N([Si](C)(C)C)C1=O1979.2Standard polar33892256
Thymine,2TMS,isomer #1CC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1733.2Semi standard non polar33892256
Thymine,2TMS,isomer #1CC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1706.2Standard non polar33892256
Thymine,2TMS,isomer #1CC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1809.4Standard polar33892256
Thymine,1TBDMS,isomer #1CC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O1824.9Semi standard non polar33892256
Thymine,1TBDMS,isomer #1CC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O1830.3Standard non polar33892256
Thymine,1TBDMS,isomer #1CC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2098.2Standard polar33892256
Thymine,1TBDMS,isomer #2CC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O1723.6Semi standard non polar33892256
Thymine,1TBDMS,isomer #2CC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O1788.3Standard non polar33892256
Thymine,1TBDMS,isomer #2CC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O2048.3Standard polar33892256
Thymine,2TBDMS,isomer #1CC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2046.2Semi standard non polar33892256
Thymine,2TBDMS,isomer #1CC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2125.6Standard non polar33892256
Thymine,2TBDMS,isomer #1CC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2003.8Standard polar33892256
Spectra
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Placenta
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.0 - 0.1 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified<5.0 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
SalivaDetected and Quantified0.655 +/- 1.44 uMAdult (>18 years old)BothNormal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified5.91 +/- 11.2 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified3.51 +/- 3.10 uMAdult (>18 years old)Both
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified2.89 +/- 4.53 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
 details
SalivaDetected and Quantified1.81 +/- 2.51 uMAdult (>18 years old)Both
Normal
    • Sugimoto et al. (...
 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified8.82 +/- 13.15 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
UrineDetected and Quantified0.202 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0-2 umol/mmol creatinineNewborn (0-30 days old)Both
Normal		 details
UrineDetected and Quantified0.10 (0.045-0.16) umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified<0.12 umol/mmol creatinineInfant (0-1 year old)Both
Normal		 details
UrineDetected and Quantified0.791 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0-9 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified0.16 (0.065-0.26) umol/mmol creatinineAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1390.0 +/- 150.0 uMAdult (>18 years old)Both
Solid tumors		 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.04 - 0.2 uMAdult (>18 years old)Not SpecifiedBeta-ureidopropionase deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
SalivaDetected and Quantified2.61 +/- 2.39 uMAdult (>18 years old)BothTemporomandibular joint disorder (TMD)
    • Sugimoto et al. (...
 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)MalePeriodontal Probing Depth details
UrineDetected and Quantified343.024 umol/mmol creatinineAdult (>18 years old)FemaleDihydropyrimidine dehydrogenase (DPD) deficiency details
UrineDetected and Quantified468.0684 umol/mmol creatinineChildren (1 - 13 years old)MaleDihydropyrimidine dehydrogenase (DPD) deficiency details
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)Download (PDF)
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. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. [PubMed:6656991 ]
  3. 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 ]
  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. Allgayer H, Kolb M, Stuber V, Kruis W: Effects of bile acids on base hydroxylation in a model of human colonic mucosal DNA. Cancer Detect Prev. 2002;26(1):85-9. [PubMed:12088208 ]
  6. Goukassian D, Gad F, Yaar M, Eller MS, Nehal US, Gilchrest BA: Mechanisms and implications of the age-associated decrease in DNA repair capacity. FASEB J. 2000 Jul;14(10):1325-34. [PubMed:10877825 ]
  7. Wassberg C, Backvall H, Diffey B, Ponten F, Berne B: Enhanced epidermal ultraviolet responses in chronically sun-exposed skin are dependent on previous sun exposure. Acta Derm Venereol. 2003;83(4):254-61. [PubMed:12926795 ]
  8. Schilsky RL, O'Laughlin K, Ratain MJ: Phase I clinical and pharmacological study of thymidine (NSC 21548) and cis-diamminedichloroplatinum(II) in patients with advanced cancer. Cancer Res. 1986 Aug;46(8):4184-8. [PubMed:3731086 ]
  9. Maskell R, Okubadejo OA, Payne RH, Pead L: Human infections with thymine-requiring bacteria. J Med Microbiol. 1978 Feb;11(1):33-45. [PubMed:621731 ]
  10. Ling G, Chadwick CA, Berne B, Potten CS, Ponten J, Ponten F: Epidermal p53 response and repair of thymine dimers in human skin after a single dose of ultraviolet radiation: effects of photoprotection. Acta Derm Venereol. 2001 May;81(2):81-6. [PubMed:11501666 ]
  11. Young AR, Sheehan JM, Chadwick CA, Potten CS: Protection by ultraviolet A and B sunscreens against in situ dipyrimidine photolesions in human epidermis is comparable to protection against sunburn. J Invest Dermatol. 2000 Jul;115(1):37-41. [PubMed:10886505 ]
  12. Maskell R, Okubadejo OA, Payne RH: Thymine-requiring bacteria associated with co-trimoxazole therapy. Lancet. 1976 Apr 17;1(7964):834-5. [PubMed:56651 ]
  13. Courdavault S, Baudouin C, Sauvaigo S, Mouret S, Candeias S, Charveron M, Favier A, Cadet J, Douki T: Unrepaired cyclobutane pyrimidine dimers do not prevent proliferation of UV-B-irradiated cultured human fibroblasts. Photochem Photobiol. 2004 Feb;79(2):145-51. [PubMed:15068027 ]
  14. Alsarra IA, Alarifi MN: Validated liquid chromatographic determination of 5-fluorouracil in human plasma. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 May 25;804(2):435-9. [PubMed:15081940 ]
  15. Castro-Gago M, Camina F, Lojo S, Rodriguez-Segade S, Rodriguez-Nunez A: Concentrations of purine nucleotides and purine and pyrimidine bases in cerebrospinal fluid of neurologically healthy children. Eur J Clin Chem Clin Biochem. 1992 Nov;30(11):761-5. [PubMed:1489848 ]
  16. Placzek M, Gaube S, Kerkmann U, Gilbertz KP, Herzinger T, Haen E, Przybilla B: Ultraviolet B-induced DNA damage in human epidermis is modified by the antioxidants ascorbic acid and D-alpha-tocopherol. J Invest Dermatol. 2005 Feb;124(2):304-7. [PubMed:15675947 ]
  17. Thienpont LM, Van Landuyt KG, Stockl D, Saeyens W, De Keukeleire D, De Leenheer AP: Evaluation of 2-iminoimidazolidin-4-one and thymine as respective internal standards for normal-phase and reversed-phase high-performance liquid chromatographic determination of creatinine in human serum. J Chromatogr B Biomed Appl. 1995 Mar 10;665(1):63-9. [PubMed:7795802 ]
  18. Rodriguez Ortner E, Hayes RB, Weissfeld J, Gelmann EP: Effect of homeodomain protein NKX3.1 R52C polymorphism on prostate gland size. Urology. 2006 Feb;67(2):311-5. Epub 2006 Jan 25. [PubMed:16442598 ]
  19. Antille C, Tran C, Sorg O, Carraux P, Didierjean L, Saurat JH: Vitamin A exerts a photoprotective action in skin by absorbing ultraviolet B radiation. J Invest Dermatol. 2003 Nov;121(5):1163-7. [PubMed:14708621 ]
  20. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

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