dTDP (C10H16N2O11P2): structure, properties and hazards

Names and identifiers

IUPAC name: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen phosphate
Synonyms: deoxy-TDP, Thymidine 5'-diphosphate, Thymidine 5'-pyrophosphate
+ 35 more
Deoxythymidine 5'-diphosphate, Thymidine 5'-(trihydrogen diphosphate), QQ3K1P45DF, DTXSID801027011, CHEBI:18075, {[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, ((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, RefChem:933037, DTXCID701511219, thymidine-5'-diphosphate, Thymidine diphosphate, thymidine-5'- diphosphate, 5'-TDP, [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen phosphate, ((2R,3S,5R)-3-Hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl)methyl trihydrogen diphosphate, TYD, thymidine 5'-(trihydrogen diphosphate) (9CI), TDP (nucleotide), Thymidine Impurity 4, UNII-QQ3K1P45DF, 5-TDP, Mono(trihydrogen diphosphate), SCHEMBL154111, Thymidine pyrophosphate (6CI), CHEMBL259724, orb1983304, 2'-Deoxythymidine-5'-diphosphate, Thymidine 5'-pyrophosphate (7CI), Thymidine 5-(trihydrogen diphosphate), DB03103, Thymidine 5-(trihydrogen pyrophosphate), Thymidine 5a(2)-(trihydrogen diphosphate), NS00015202, C00363, Thymidine 5'-(trihydrogen pyrophosphate) (8CI)
Molecular formula: C₁₀H₁₆N₂O₁₁P₂
Empirical formula: C₁₀H₁₆N₂O₁₁P₂
Molecular weight: 402.19 g/mol
Exact mass: 402.02293
CAS number: 491-97-4
PubChem CID: 164628
Canonical SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
Isomeric SMILES: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)O)O
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
InChIKey: UJLXYODCHAELLY-XLPZGREQSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms: 25
Rings: 2
Aromatic rings: 1
Fraction sp³ carbons (Fsp3): 0.6
H-bond donors: 5
H-bond acceptors: 8 computed here · PubChem 11
Rotatable bonds: 6
TPSA (Å²): 197.6 computed here · PubChem 192
Formal charge: 0
XLogP3: -3.9 PubChem
Complexity: 688 PubChem
Stereocenters: 3 defined, 1 undefinedCIP: C5: R · C7: S · C9: R · P12: undefined
Double-bond geometry: None specified
Point group: C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

C29.86%
H4.01%
N6.97%
O43.76%
P15.40%

Isotope pattern

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P: -1.28 Crippen (Wildman and Crippen 1999)
log S (water solubility): -1.31 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 4 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 402.19
log P ≤ 5 (Crippen): -1.28
H-bond donors ≤ 5: 5
H-bond acceptors ≤ 10: 8

Passes all four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

No GHS hazard classification was found in the sources.

Safety data sheets on the supplier’s page: InvivoChem, Smolecule, EvitaChem.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

[1]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[2]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
[3]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
[4]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
·Literature on PubChem

Data last updated 2026-10-14.

Similar structures

Tanimoto similarity on Morgan fingerprints (radius 2) with RDKit 2026.09, at least 45%.