dCDP
Athanor · official
C9H15N3O10P2 · 387.18 g/mol
IUPAC name: [(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Names and identifiers
- IUPAC name
- [(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
- Synonyms
- 2'-deoxycytidine diphosphate, Deoxycytidine 5'-diphosphate, 2'-Deoxycytidine 5'-diphosphate
+ 33 more
M07S1BKN37, CHEBI:28846, [({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid, (((((2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl)methoxy)(hydroxy)phosphoryl)oxy)phosphonic acid, RefChem:919698, Deoxycytidine diphosphate, Deoxy-CDP, 2'-deoxycytidine-5'-diphosphate, 1beta-Ribofuranosylcytosine diphosphate, D-, 2'-deoxycytidine 5'-(trihydrogen diphosphate), ((2R,3S,5R)-5-(4-Amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxytetrahydrofuran-2-yl)methyl trihydrogen diphosphate, D-1beta-Ribofuranosylcytosine diphosphate, Cytidine 5'-(trihydrogen diphosphate), 2'-deoxy-, UNII-M07S1BKN37, YYY, Cytidine Impurity 11, SCHEMBL158324, 2'-deoxy-Cytidine pyrophosphate, SCHEMBL28678281, FTDHDKPUHBLBTL-SHYZEUOFSA-N, DTXSID301027111, 2'-deoxy-Cytidine 5'-pyrophosphate, Cytidine, 2'-deoxy-, pyrophosphate, Cytidine, 2'-deoxy-, 5'-pyrophosphate, [(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate, delta-1beta-Ribofuranosylcytosine diphosphate, NS00014661, C00705, Cytidine, 2'-deoxy-, 5'-(trihydrogen pyrophosphate), Q55168710, 2(1H)-pyrimidinone, 4-amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-, 4-amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone, 4-amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone
- Molecular formula
- C9H15N3O10P2
- Empirical formula
- C9H15N3O10P2
- Molecular weight
- 387.18 g/mol
- Exact mass
- 387.02327
- CAS number
- 800-73-7
- PubChem CID
- 150855
- Canonical SMILES
- C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)O)O
- Isomeric SMILES
- C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)O)O
- InChI
- InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
- InChIKey
- FTDHDKPUHBLBTL-SHYZEUOFSA-N
- Molfile
Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.
Calculated
- Heavy atoms
- 24
- Rings
- 2
- Aromatic rings
- 1
- Fraction sp³ carbons (Fsp3)
- 0.56
- H-bond donors
- 5
- H-bond acceptors
- 9 computed here · PubChem 10
- Rotatable bonds
- 6
- TPSA (Ų)
- 203.7 computed here · PubChem 201
- Formal charge
- 0
- XLogP3
- -4.5 PubChem
- Complexity
- 660 PubChem
- Stereocenters
- 3 defined, 1 undefinedCIP: C6: R · C8: S · C10: R · P13: 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
- C27.92%
- H3.91%
- N10.85%
- O41.32%
- P16.00%
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
- -1.3 Crippen (Wildman and Crippen 1999)
- log S (water solubility)
- -1.21 ESOL (Delaney 2004), log mol/L
- Synthetic accessibility
- 4.08 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)
Drug-likeness: Lipinski’s rule of five
- Molecular weight ≤ 500: 387.18
- log P ≤ 5 (Crippen): -1.3
- H-bond donors ≤ 5: 5
- H-bond acceptors ≤ 10: 9
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: Quality Control Solutions (QCS Standards), AiFChem, an XtalPi Company, BOC Sciences.
Always read the supplier’s safety data sheet before working with it.
Spectra
- MS-MSHuman Metabolome Database (HMDB) (LC-ESI-QTOF · negative) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Positive) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Negative)
- LC-MSMassBank Europe (UPLC Q-Tof Premier, Waters · LC-ESI-QTOF · POSITIVE) · MassBank Europe (UPLC Q-Tof Premier, Waters · LC-ESI-QTOF · POSITIVE) · MassBank Europe (UPLC Q-Tof Premier, Waters · LC-ESI-QTOF · NEGATIVE) · MassBank of North America (MoNA) (Q-Tof Premier, Waters · LC-Q-TOF/MS · ESI) · MassBank of North America (MoNA) (Q-Tof Premier, Waters · LC-Q-TOF/MS · ESI) · MassBank of North America (MoNA) (Q-Tof Premier, Waters · LC-Q-TOF/MS · ESI)
- Other MSMassBank of North America (MoNA) (qTof · positive) · MassBank of North America (MoNA) (qTof · negative) · MassBank of North America (MoNA) (Orbitrap · negative)
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]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
- [2]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
- [3]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.