Showing metabocard for dTDP (BMDB0001274)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:43:28 UTC
Update Date2020-05-21 16:29:01 UTC
BMDB IDBMDB0001274
Secondary Accession Numbers
  • BMDB01274
Metabolite Identification
Common 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.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
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
Chemical FormulaC10H16N2O11P2
Average Molecular Weight402.1884
Monoisotopic Molecular Weight402.022932388
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
Traditional NamedTDP
CAS Registry Number491-97-4
SMILES
CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O
InChI Identifier
InChI=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
Chemical Taxonomy
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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004m-6922000000-78987adf8e4b2b4baa77View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00dm-9341200000-af3e3a557688731137d2View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0kdi-9720700000-003f87d03143415a6bf9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-f02dc55e07c9935275d9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4901000000-bc16523808594ec9a806View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-2199218952cf36a3e3a2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-2607900000-696f76b41235895dc296View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9801000000-9bc55b2280dfcf3aed1dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d33e29452de0777eaa0dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-1100900000-bedafc8a6d3579ef1476View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9102100000-8cad78608dae5988a8c1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0ff3218786dbaaac7deaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0920500000-ccf96f505a327015ed67View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2910000000-857f636dcd89f8378f36View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-2910000000-b95a62414e3f309b00bbView in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001274
DrugBank IDDB03103
Phenol Explorer Compound IDNot Available
FooDB IDFDB022528
KNApSAcK IDC00019696
Chemspider ID144320
KEGG Compound IDC00363
BioCyc IDTDP
BiGG ID34750
Wikipedia LinkThymidine_diphosphate
METLIN ID6129
PubChem Compound164628
PDB IDNot Available
ChEBI ID18075
References
Synthesis ReferenceRupprath, Carsten; Kopp, Maren; Hirtz, Dennis; Mueller, Rolf; Elling, Lothar. An enzyme module system for in situ regeneration of deoxythymidine 5'-diphosphate (dTDP)-activated deoxy sugars. Advanced Synthesis & Catalysis (2007), 349(8+9), 1489-1496.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. dTDP-D-glucose 4,6-dehydratase
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Not Available
Gene Name:
TGDS
Uniprot ID:
A6QLW2
Molecular weight:
40666.0
Enzyme Details
2. Nucleoside diphosphate kinase 7
General function:
Nucleotide transport and metabolism
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
Gene Name:
NME7
Uniprot ID:
Q5E9Y9
Molecular weight:
42599.0
Reactions
dTDP + Adenosine triphosphate → Thymidine 5'-triphosphate + ADPdetails
Enzyme Details
3. Thymidylate synthase
General function:
Nucleotide transport and metabolism
Specific function:
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name:
TYMS
Uniprot ID:
Q2TA32
Molecular weight:
39785.0
Reactions
5-Thymidylic acid + Adenosine triphosphate → dTDP + ADPdetails
Enzyme Details
4. Calcium activated nucleotidase 1
General function:
Not Available
Specific function:
Not Available
Gene Name:
CANT1
Uniprot ID:
E1BGL5
Molecular weight:
44706.0
Reactions
dTDP + Water → 5-Thymidylic acid + Hydrogen phosphatedetails
Thymidine 5'-triphosphate + Water → dTDP + Hydrogen phosphatedetails