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Showing NP-Card for Thymine (NP0001126)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:42:30 UTC
NP-MRD IDNP0001126
Secondary Accession NumbersNone
Natural Product 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 NP0001126 (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
Download

3D MOL for NP0001126 (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
Download

3D SDF for NP0001126 (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>
NP0001126

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0001126 (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
Download

PDB for NP0001126 (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
Download

3D PDB for NP0001126 (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 NP0001126 (Thymine)

CC1=CNC(=O)NC1=O
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INCHI for NP0001126 (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 JSmol
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 Mass126.1133 Da
Monoisotopic Mass126.04293 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 400 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-03View Spectrum
Species
Species of Origin
Species NameSourceReference
Amphimedon viridisLOTUS Database
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Crocus sativusKNApSAcK Database
Dromaius novaehollandiaeFooDB
Eleutherococcus giraldiiLOTUS Database
Equisetum hiemaleKNApSAcK Database
Equus caballusFooDB
Gallus gallusFooDB
Gastrodia elataLOTUS Database
Geodia japonicaLOTUS Database
Homo sapiensLOTUS Database
Huperzia serrataLOTUS Database
Junceella juncea-
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Litoria verreauxiiLOTUS Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Nothapodytes nimmonianaLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
Ophiocordyceps sinensisLOTUS Database
OryctolagusFooDB
Ovis ariesFooDB
Pancratium maritimumLOTUS Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Phomopsis velataLOTUS Database
Pinellia pedatisectaKNApSAcK Database
Salmonella entericaLOTUS Database
Streptomyces piomogenusLOTUS Database
Struthio camelusFooDB
Stylissa massaLOTUS Database
Subergorgia suberosa-
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Trypanosoma bruceiLOTUS Database
Viscum coloratumKNApSAcK Database
Wallemia sebiLOTUS Database
Xanthium strumariumLOTUS Database
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Phakellia mauritianaKNApSAcK Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point320 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.82 mg/mLYalkowsky, S. H., & Dannenfelser, R. M. (1992). Aquasol database of aqueous solubility. College of Pharmacy, University of Arizona, Tucson, AZ, 189.
LogP-0.62Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted 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
HMDB IDHMDB0000262
DrugBank IDDB03462
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021922
KNApSAcK IDC00001511
Chemspider ID1103
KEGG Compound IDC00178
BioCyc IDTHYMINE
BiGG ID34151
Wikipedia LinkThymine
METLIN ID290
PubChem Compound1135
PDB IDNot Available
ChEBI ID17821
Good Scents IDrw1289321
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. 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 ]
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