CDP
Athanor · official
C9H15N3O11P2 · 403.18 g/mol
IUPAC name: [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Also called cytidine diphosphate
Names and identifiers
- IUPAC name
- [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
- Synonyms
- cytidine diphosphate, cytidine-5'-diphosphate, Cytidine diphosphate
+ 35 more
5'-CDP, 1ZH821MXU5, [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate, DTXSID501014481, ((2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl)methyl phosphono hydrogen phosphate, Diphosphate, Cytidine, RefChem:130309, DTXCID001437064, disodium;((5-(4-amino-2-keto-pyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl)methoxy-oxido-phosphoryl) hydrogen phosphate, Cytidine 5'-diphosphate, Cytidine 5'-(trihydrogen diphosphate), Cytidine coenzyme, Cytidine 5'-pyrophosphate, Cytidine 5'-diphosphoric acid, Cytidine 5'-pyrophosphoric acid, Sulbactum sodium, cytidine-diphosphate, BRN 0063920, Cytidine pyrophosphate, CYTIDINE, 5'-(TRIHYDROGEN PYROPHOSPHATE), CHEMBL425252, Cytidine 5'-(trihydrogen pyrophosphate), [({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid, Cytidine 5'-diphosphate disodium, ((2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl trihydrogen diphosphate, C9H15N3O11P2, EINECS 200-557-1, UNII-1ZH821MXU5, Cyclazosin Impurity 2, Cytidine 5 -diphosphate, [3h]cytidine diphosphate, bmse000272, Cytidine 5''-pyrophosphate, 4-25-00-03675 (Beilstein Handbook Reference), Cytidine pyrophosphate (6CI)
- Molecular formula
- C9H15N3O11P2
- Empirical formula
- C9H15N3O11P2
- Molecular weight
- 403.18 g/mol
- Exact mass
- 403.01818
- CAS number
- 63-38-7
- PubChem CID
- 6132
- Canonical SMILES
- C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
- Isomeric SMILES
- C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)O)O)O
- InChI
- InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
- InChIKey
- ZWIADYZPOWUWEW-XVFCMESISA-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)
- 0.56
- H-bond donors
- 6
- H-bond acceptors
- 10 computed here · PubChem 11
- Rotatable bonds
- 6
- TPSA (Ų)
- 223.9 computed here · PubChem 222
- Formal charge
- 0
- XLogP3
- -4.5 PubChem
- Complexity
- 690 PubChem
- Stereocenters
- 4 defined, 1 undefinedCIP: C6: R · C8: R · P11: undefined · C19: S · C21: R
- 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
- C26.81%
- H3.75%
- N10.42%
- O43.65%
- P15.36%
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
- -2.33 Crippen (Wildman and Crippen 1999)
- log S (water solubility)
- -0.65 ESOL (Delaney 2004), log mol/L
- Synthetic accessibility
- 4.14 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)
Drug-likeness: Lipinski’s rule of five
- Molecular weight ≤ 500: 403.18
- log P ≤ 5 (Crippen): -2.33
- H-bond donors ≤ 5: 6
- H-bond acceptors ≤ 10: 10
Breaks 1 of the 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: DC Chemicals, BOC Sciences, Smolecule.
Always read the supplier’s safety data sheet before working with it.
Spectra
- 1H NMRHuman Metabolome Database (HMDB) (Bruker · D2O) · SpectraBase
- 13C NMRHuman Metabolome Database (HMDB) (Bruker · D2O) · SpectraBase
- 31P NMRSpectraBase (Bruker HX-90)
- MS-MSHuman Metabolome Database (HMDB) (Positive) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Positive) · Human Metabolome Database (HMDB) (Positive) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Negative)
- LC-MSMassBank Europe (impact II · LC-ESI-QTOF · POSITIVE) · MassBank Europe (impact II · LC-ESI-QTOF · POSITIVE) · MassBank Europe (impact II · LC-ESI-QTOF · POSITIVE) · MassBank Europe (impact II · LC-ESI-QTOF · POSITIVE) · MassBank Europe (impact II · LC-ESI-QTOF · POSITIVE) · MassBank Europe (impact II · LC-ESI-QTOF · POSITIVE)
- Other MSMassBank of North America (MoNA) (TQD, Waters · Flow-injection QqQ/MS · ESI) · MassBank of North America (MoNA) (TQD, Waters · Flow-injection QqQ/MS · ESI) · MassBank of North America (MoNA) (TQD, Waters · Flow-injection QqQ/MS · ESI)
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]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
- [3]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
- [4]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
- [5]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.