Record Information
Version1.0
Creation date2011-09-21 00:15:25 UTC
Update date2020-09-17 15:38:54 UTC
Primary IDFDB022528
Secondary Accession NumbersNot Available
Chemical Information
FooDB NamedTDP
DescriptiondTDP, also known as deoxy-TDP, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dTDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dTDP exists in all living species, ranging from bacteria to humans. Outside of the human body, dTDP has been detected, but not quantified in, several different foods, such as brussel sprouts, wheats, herbs and spices, papaya, and red raspberries. This could make dTDP a potential biomarker for the consumption of these foods. A thymidine phosphate having a diphosphate group at the 5'-position.
CAS Number491-97-4
Structure
Thumb
Synonyms
SynonymSource
2'-Deoxyribosylthymine 5'-(trihydrogen diphosphate)ChEBI
Deoxy-TDPChEBI
Deoxythymidine 5'-diphosphateChEBI
Thymidine 5'-diphosphateChEBI
Thymidine 5'-pyrophosphateChEBI
THYMIDINE-5'- diphosphATEChEBI
2'-Deoxyribosylthymine 5'-(trihydrogen diphosphoric acid)Generator
Deoxythymidine 5'-diphosphoric acidGenerator
Thymidine 5'-diphosphoric acidGenerator
Thymidine 5'-pyrophosphoric acidGenerator
THYMIDINE-5'- diphosphoric acidGenerator
TDPHMDB
2'-Deoxyribosylthymine 5'-(trihydrogen diate)ChEBI
2'-Deoxyribosylthymine 5'-(trihydrogen diic acid)Generator
Deoxy-tdphmdb
Deoxythymidine 5'-diateChEBI
Deoxythymidine 5'-diic acidGenerator
dTDPhmdb
Thymidine 5'-diateChEBI
Thymidine 5'-diic acidGenerator
Thymidine 5'-pyroateChEBI
Thymidine 5'-pyroic acidGenerator
THYMIDINE-5'- diATEChEBI
THYMIDINE-5'- diic acidGenerator
Predicted Properties
PropertyValueSource
Water Solubility6.94 g/LALOGPS
logP-0.87ALOGPS
logP-1.7ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area192.16 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity77.16 m³·mol⁻¹ChemAxon
Polarizability32.12 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC10H16N2O11P2
IUPAC name{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}phosphonic acid
InChI IdentifierInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChI KeyUJLXYODCHAELLY-XLPZGREQSA-N
Isomeric SMILESCC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O
Average Molecular Weight402.1884
Monoisotopic Molecular Weight402.022932388
Classification
Description Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Lactam
  • Urea
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Biological location:

Source:

Role

Industrial application:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSdTDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-004m-6922000000-78987adf8e4b2b4baa77Spectrum
Predicted GC-MSdTDP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00dm-9341200000-af3e3a557688731137d2Spectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0kdi-9720700000-003f87d03143415a6bf9Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-f02dc55e07c9935275d9Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4901000000-bc16523808594ec9a806Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-2199218952cf36a3e3a2Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-2607900000-696f76b41235895dc296Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9801000000-9bc55b2280dfcf3aed1dSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d33e29452de0777eaa0dSpectrum
NMRNot Available
ChemSpider ID144320
ChEMBL IDCHEMBL259724
KEGG Compound IDC00363
Pubchem Compound ID164628
Pubchem Substance IDNot Available
ChEBI ID18075
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB01274
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID34750
KNApSAcK IDNot Available
HET IDTYD
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
NameGene NameUniProt ID
Uridine-cytidine kinase-like 1UCKL1Q9NWZ5
Polyribonucleotide nucleotidyltransferase 1, mitochondrialPNPT1Q8TCS8
Thymidylate kinaseDTYMKP23919
Nucleoside diphosphate kinaseNME4A2IDD0
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046 map00240
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference