ddCTP
Athanor · official
C9H16N3O12P3 · 451.16 g/mol
IUPAC name: [[(2S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
Also called dideoxycytidine triphosphate, ddNTP
Names and identifiers
- IUPAC name
- [[(2S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
- Synonyms
- dideoxycytidine triphosphate, ddNTP, 2',3'-Dideoxycytidine 5'-triphosphate
+ 36 more
2',3'-ddCTP, Triphosphoric acid, P-((5-(4-amino-2-oxo-1(2H)-pyrimidinyl)tetrahydro-2-furanyl)methyl) ester, (2S-cis)-, ddCTP-2',3', RefChem:919700, Dideoxycytidine 5'-Triphosphate, [[(2S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate, Cytidine 5'-(tetrahydrogen triphosphate), 2',3'-dideoxy-, DideoxyCTP, 2',3'-dideoxycytidine-5'-triphosphate, ((2S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)tetrahydrofuran-2-yl)methyl tetrahydrogen triphosphate, ddC-TP, ARLKCWCREKRROD-POYBYMJQSA-N, Liposomal(ddCTP), DTXSID701343965, [[(2S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate, 2',3'-Dideoxycytidine triphosphate, Zalcitabine triphosphate, orb65196, orb638822, SCHEMBL210922, orb1690371, orb1733965, orb1734210, orb2702618, orb2702619, CHEMBL1201384, EX-A9031S, BDBM50483420, EBC-14298, AKOS040758264, 2',3'-Dideoxycytosine-5'-triphosphate, 2',3'-dideoxy-cytidine-5'-triphosphate, DA-52366, HY-137697, CS-0141252, T40759
- Molecular formula
- C9H16N3O12P3
- Empirical formula
- C9H16N3O12P3
- Molecular weight
- 451.16 g/mol
- Exact mass
- 450.99468
- CAS number
- 93039-00-4
- PubChem CID
- 119119
- Canonical SMILES
- C1CC(OC1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
- Isomeric SMILES
- C1C[C@@H](O[C@@H]1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
- InChI
- InChI=1S/C9H16N3O12P3/c10-7-3-4-12(9(13)11-7)8-2-1-6(22-8)5-21-26(17,18)24-27(19,20)23-25(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
- InChIKey
- ARLKCWCREKRROD-POYBYMJQSA-N
- Molfile
Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.
Calculated
- Heavy atoms
- 27
- Rings
- 2
- Aromatic rings
- 1
- Fraction sp³ carbons (Fsp3)
- 0.56
- H-bond donors
- 5
- H-bond acceptors
- 10 computed here · PubChem 12
- Rotatable bonds
- 8
- TPSA (Ų)
- 230 computed here · PubChem 228
- Formal charge
- 0
- XLogP3
- -5.5 PubChem
- Complexity
- 792 PubChem
- Stereocenters
- 2 defined, 2 undefinedCIP: C6: R · C9: S · P12: undefined · P16: 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
- C23.96%
- H3.57%
- N9.31%
- O42.55%
- P20.60%
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
- -0.15 Crippen (Wildman and Crippen 1999)
- log S (water solubility)
- -2.18 ESOL (Delaney 2004), log mol/L
- Synthetic accessibility
- 4.3 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)
Drug-likeness: Lipinski’s rule of five
- Molecular weight ≤ 500: 451.16
- log P ≤ 5 (Crippen): -0.15
- H-bond donors ≤ 5: 5
- H-bond acceptors ≤ 10: 10
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: Biorbyt, CATO Research Chemicals Inc., AA BLOCKS.
Always read the supplier’s safety data sheet before working with it.
Literature
Reading PubChem, OpenAlex and GSRS…
Bioactivity
Reading ChEMBL…
References
- ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
- ·Literature on PubChem
Data last updated 2026-10-14.