Record Information
Version2.0
Creation Date2012-05-31 13:48:55 -0600
Update Date2015-06-03 15:53:53 -0600
Secondary Accession Numbers
  • ECMDB01274
Identification
Name:dTDP
DescriptiondTDP is an intermediate in the synthesis and breakdown of DNA. Thymidylate kinase (EC 2.7.4.9; ATP:dTMP phosphotransferase) catalyzes the phosphorylation of dTMP (to form dTDP) in the dTTP synthesis pathway for DNA synthesis. (OMIM 188345
Structure
Thumb
Synonyms:
  • Deoxy-TDP
  • Deoxythymidine 5'-diphosphate
  • Deoxythymidine 5'-diphosphoric acid
  • DTDP
  • TDP
  • Thymidine 5'-(trihydrogen diphosphate) (9CI)
  • Thymidine 5'-(trihydrogen diphosphoric acid) (9ci)
  • Thymidine 5'-diphosphate
  • Thymidine 5'-diphosphoric acid
  • Thymidine 5'-pyrophosphate
  • Thymidine 5'-pyrophosphoric acid
  • Thymidine-5'-diphosphate
  • Thymidine-5'-diphosphoric acid
  • Thymidine-diphosphate
  • Thymidine-diphosphoric acid
Chemical Formula:C10H16N2O11P2
Weight:Average: 402.1884
Monoisotopic: 402.022932388
InChI Key:UJLXYODCHAELLY-XLPZGREQSA-N
InChI: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
CAS number:491-97-4
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 IUPAC Name:dTDP
SMILES:CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O
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
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Polarizability32.13 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine triphosphate + dTDP <> ADP + Thymidine 5'-triphosphate
Adenosine triphosphate + 5-Thymidylic acid <> ADP + dTDP
Deoxythymidine diphosphate-L-rhamnose + Kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA > dTDP + Hydrogen ion + inner core oligosaccharide lipid A (E coli)
dTDP-4-Acetamido-4,6-dideoxy-D-galactose + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate > dTDP + Hydrogen ion + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
Thymidine 5'-triphosphate + Cytidine <> dTDP + Cytidine monophosphate
Thymidine 5'-triphosphate + Uridine <> dTDP + Uridine 5'-monophosphate
a lipopolysaccharide + Deoxythymidine diphosphate-L-rhamnose a rhamnosyl lipopolysaccharide + dTDP
dTDP + Adenosine triphosphate > Thymidine 5'-triphosphate + ADP
5-Thymidylic acid + Adenosine triphosphate > dTDP + ADP
Undecaprenyl phosphate + dTDP-4-Acetamido-4,6-dideoxy-D-galactose > Hydrogen ion + undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate + dTDP
Adenosine triphosphate + dTDP > Adenosine diphosphate + Thymidine 5'-triphosphate + ADP
Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate pyrophosphate + TDP-Fuc4NAc + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate > Hydrogen ion + dTDP + Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
Adenosine triphosphate + 5 5-Thymidylic acid <> ADP + dTDP
Adenosine triphosphate + 5 5-Thymidylic acid <> ADP + dTDP
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
Secondary Metabolites: enterobacterial common antigen biosynthesisPW000959 ThumbThumb?image type=greyscaleThumb?image type=simple
Secondary Metabolites: enterobacterial common antigen biosynthesis 2PW002045 ThumbThumb?image type=greyscaleThumb?image type=simple
Secondary Metabolites: enterobacterial common antigen biosynthesis 3PW002046 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • enterobacterial common antigen biosynthesis ECASYN-PWY
  • pyrimidine deoxyribonucleotides de novo biosynthesis I PWY0-166
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
378± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
Find out more about how we convert literature concentrations.
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
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
References
References:
  • Ahmed IH, Manning G, Wassenaar TM, Cawthraw S, Newell DG: Identification of genetic differences between two Campylobacter jejuni strains with different colonization potentials. Microbiology. 2002 Apr;148(Pt 4):1203-12. Pubmed: 11932464
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Bialkowski K, Kasprzak KS: Inhibition of 8-oxo-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase (8-oxo-dGTPase) activity of the antimutagenic human MTH1 protein by nucleoside 5'-diphosphates. Free Radic Biol Med. 2003 Sep 15;35(6):595-602. Pubmed: 12957652
  • Costantini P, Belzacq AS, Vieira HL, Larochette N, de Pablo MA, Zamzami N, Susin SA, Brenner C, Kroemer G: Oxidation of a critical thiol residue of the adenine nucleotide translocator enforces Bcl-2-independent permeability transition pore opening and apoptosis. Oncogene. 2000 Jan 13;19(2):307-14. Pubmed: 10645010
  • Dahlmann N: Human serum thymidine triphosphate nucleotidohydrolase: purification and properties of a new enzyme. Biochemistry. 1982 Dec 21;21(26):6634-9. Pubmed: 6297538
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Kuo SY, Ho CM, Chen WC, Jan CR: Sulfhydryl modification by 4,4'-dithiodipyridine induces calcium mobilization in human osteoblast-like cells. Arch Toxicol. 2003 Nov;77(11):630-7. Epub 2003 Aug 20. Pubmed: 12928766
  • Kuo SY, Jiann BP, Lu YC, Chang HT, Chen WC, Huang JK, Jan CR: Thiol oxidation by 2,2'-dithiodipyridine induced calcium mobilization in MG63 human osteosarcoma cells. Life Sci. 2003 Feb 28;72(15):1733-43. Pubmed: 12559394
  • Ramaswamy SV, Amin AG, Goksel S, Stager CE, Dou SJ, El Sahly H, Moghazeh SL, Kreiswirth BN, Musser JM: Molecular genetic analysis of nucleotide polymorphisms associated with ethambutol resistance in human isolates of Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2000 Feb;44(2):326-36. Pubmed: 10639358
  • Riener CK, Kada G, Gruber HJ: Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4'-dithiodipyridine. Anal Bioanal Chem. 2002 Jul;373(4-5):266-76. Epub 2002 Jun 6. Pubmed: 12110978
  • Sheu SJ, Wu SN: Mechanism of inhibitory actions of oxidizing agents on calcium-activated potassium current in cultured pigment epithelial cells of the human retina. Invest Ophthalmol Vis Sci. 2003 Mar;44(3):1237-44. Pubmed: 12601054
  • Tomioka H: [Prospects for development of new antituberculous drugs] Kekkaku. 2002 Aug;77(8):573-84. Pubmed: 12235850
  • Vallon O: New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure. Proteins. 2000 Jan 1;38(1):95-114. Pubmed: 10651042
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Xu Y, Singh KV, Qin X, Murray BE, Weinstock GM: Analysis of a gene cluster of Enterococcus faecalis involved in polysaccharide biosynthesis. Infect Immun. 2000 Feb;68(2):815-23. Pubmed: 10639451
Synthesis Reference:Rupprath, 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), 1489-149
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID18075
HMDB IDHMDB01274
Pubchem Compound ID164628
Kegg IDC00363
ChemSpider ID144320
Wikipedia IDThymidine_diphosphate
BioCyc IDTDP
EcoCyc IDTDP
Ligand ExpoTYD

Enzymes

General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth
Gene Name:
tmk
Uniprot ID:
P0A720
Molecular weight:
23783
Reactions
ATP + dTMP = ADP + dTDP.
General function:
Involved in nucleoside diphosphate kinase activity
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
Gene Name:
ndk
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
udk
Uniprot ID:
P0A8F4
Molecular weight:
24353
Reactions
ATP + uridine = ADP + UMP.
ATP + cytidine = ADP + CMP.
General function:
Involved in fucosyltransferase activity
Specific function:
Catalyzes the synthesis of Und-PP-GlcNAc-ManNAcA-Fuc4NAc (Lipid III), the third lipid-linked intermediate involved in ECA synthesis
Gene Name:
wecF
Uniprot ID:
P56258
Molecular weight:
40639
Reactions
TDP-Fuc4NAc + Und-PP-GlcNAc-ManNAcA = TDP + Und-PP-GlcNAc-ManNAcA-Fuc4NAc.
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Uniprot ID:
P69441
Molecular weight:
23586
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in protein binding
Specific function:
Specific function unknown
Gene Name:
rfaS
Uniprot ID:
P27126
Molecular weight:
36730

Transporters

General function:
Involved in nucleoside diphosphate kinase activity
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
Gene Name:
ndk
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.