dCMP (C9H14N3O7P): structure, properties and hazards

Names and identifiers

IUPAC name: [(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate
Synonyms: deoxycytidine monophosphate, deoxycytidylic acid, 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
+ 35 more
2'-Deoxycytidine 5'-monophosphate, Deoxycytidylate, 5'-Cytidylic acid, 2'-deoxy-, W7A9174XQL, DTXSID20908251, [(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate, {[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid, Acid, Deoxycytidylic, Monophosphate, Deoxycytidine, (((2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl)methoxy)phosphonic acid, ((2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl)methyl dihydrogen phosphate, RefChem:7185, DTXCID301376708, 2'-Deoxycytidine-5'-monophosphoric acid, 2'-deoxy-5'-cytidylic acid, 1njc, 1nje, Deoxycytidine-5'-monophosphoric acid, MFCD00006546, deoxycytidine-phosphate, SCHEMBL48317, deoxycytidine dihydrogen phosphate, 2'-deoxycytosine 5'-monophosphate, 2'-Deoxycytidine 5'-Monophosphate Hydrate, ((2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxytetrahydrofuran-2-yl)methyl dihydrogen phosphate, AS-64039, C9H14N3O7P, 2'-Deoxycytidine 5'-monophosphate, Sigma Grade, >=95.0%, 2_-Deoxycytidine 5_-Monophosphate, 2 inverted exclamation marka-Deoxycytidine 5 inverted exclamation marka-monophosphate, dCMP.H2, UNII-W7A9174XQL, 1nja, EINECS 213-849-9, Diquafosol Impurity 27
Molecular formula: C₉H₁₄N₃O₇P
Empirical formula: C₉H₁₄N₃O₇P
Molecular weight: 307.2 g/mol
Exact mass: 307.05694
CAS number: 1032-65-1
PubChem CID: 13945
Canonical SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
Isomeric SMILES: C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
InChI: InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey: NCMVOABPESMRCP-SHYZEUOFSA-N
Molfile

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

Calculated

Heavy atoms: 20
Rings: 2
Aromatic rings: 1
Fraction sp³ carbons (Fsp3): 0.56
H-bond donors: 4
H-bond acceptors: 7
Rotatable bonds: 4
TPSA (Å²): 157.1 computed here · PubChem 155
Formal charge: 0
XLogP3: -3.4 PubChem
Complexity: 502 PubChem
Stereocenters: 3 definedCIP: C6: R · C8: S · C10: 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

C35.19%
H4.59%
N13.68%
O36.46%
P10.08%

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: -1.42 Crippen (Wildman and Crippen 1999)
log S (water solubility): -0.81 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 3.76 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 307.2
log P ≤ 5 (Crippen): -1.42
H-bond donors ≤ 5: 4
H-bond acceptors ≤ 10: 7

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

Warning

Most widely reported: 2 company reports to ECHA. Source [1].

Harmful or irritant

H302Harmful if swallowed (50% of reports)
H312Harmful in contact with skin (50% of reports)
H332Harmful if inhaled (50% of reports)

Precautionary statements: P261, P264, P270, P271, P280, P301+P317, P302+P352, P304+P340, P317, P321, P330, P362+P364, P501

View all classifications (2)

[1] European Chemicals Agency (ECHA)This chemical does not meet GHS hazard criteria for 50% (1 of 2) of reports.
[1] European Chemicals Agency (ECHA) · 2 reports · WarningH302, H312, H332

Safety data sheets on the supplier’s page: CymitQuimica, Aladdin Scientific, Sinfoo Biotech.

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]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[2]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
[3]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[4]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
[5]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
[6]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%.