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DNA repeating unit

Athanor · official

C10H15N5O9P2 · 411.2 g/mol

IUPAC name: [(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] dihydrogen phosphate

Also called DNA, deoxyribonucleotide, phosphodiester backbone, deoxyadenosine phosphate unit

Nucleic acid parts
Open in Athanor
The structure of DNA repeating unit
Drawn from its SMILES with RDKit

Names and identifiers

IUPAC name
[(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] dihydrogen phosphate
Synonyms
DNA, deoxyribonucleotide, phosphodiester backbone
+ 10 more

deoxyadenosine phosphate unit, 2'-deoxyadenosine-3',5'-diphosphate, RefChem:908422, CHEMBL1230817, 2'-DEOXY-ADENOSINE-3'-5'-DIPHOSPHATE, SCHEMBL375910, orb3180077, BDBM50608209, 2'-deoxyadenosine 3',5'-bis(dihydrogen phosphate), Q27457216

Molecular formula
C10H15N5O9P2
Empirical formula
C10H15N5O9P2
Molecular weight
411.2 g/mol
Exact mass
411.03450
CAS number
16174-58-6
PubChem CID
14252049
Canonical SMILES
C1C(C(OC1N2C=NC3=C(N=CN=C32)N)COP(=O)(O)O)OP(=O)(O)O
Isomeric SMILES
C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)N)COP(=O)(O)O)OP(=O)(O)O
InChI
InChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(24-26(19,20)21)6(23-7)2-22-25(16,17)18/h3-7H,1-2H2,(H2,11,12,13)(H2,16,17,18)(H2,19,20,21)/t5-,6+,7+/m0/s1
InChIKey
GOZKRKUVKAXOEP-RRKCRQDMSA-N
Molfile

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

Calculated

Heavy atoms
26
Rings
3
Aromatic rings
2
Fraction sp³ carbons (Fsp3)
0.5
H-bond donors
5
H-bond acceptors
9 computed here · PubChem 13
Rotatable bonds
6
TPSA (Ų)
212.4 computed here · PubChem 212
Formal charge
0
XLogP3
-3.1 PubChem
Complexity
601 PubChem
Stereocenters
3 definedCIP: C11: R · C13: S · C19: 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

  • C29.21%
  • H3.68%
  • N17.03%
  • O35.02%
  • P15.07%

Isotope pattern

100%411.03413%412.0372.7%413.039414.041

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
-0.72 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-1.8 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
3.99 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 411.2
  • log P ≤ 5 (Crippen): -0.72
  • 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: Biorbyt.

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

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  2. ·Literature on PubChem

Data last updated 2026-10-14.