dGDP
Athanor · official
C10H15N5O10P2 · 427.2 g/mol
IUPAC name: [(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Names and identifiers
- IUPAC name
- [(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
- Synonyms
- 2'-deoxyguanosine-5'-diphosphate, [(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate, ((2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl)methyl phosphono hydrogen phosphate
+ 23 more
RefChem:439636, 2'-Deoxyguanosine 5'-diphosphate, Deoxyguanosine 5'-diphosphate, deoxyguanosine diphosphate, CHEMBL1232205, CHEBI:28862, 2'-deoxyguanosine 5'-(trihydrogen diphosphate), 2'-Deoxy-GDP, deoxyguanosine-diphosphate, 5'-dGDP, [({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid, Guanosine Impurity 7, SCHEMBL157937, DTXSID601027110, ((2R,3S,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl)methyl trihydrogen diphosphate, BDBM50035297, DB03491, PD059735, NS00015101, C00361, Q27103932, 2invertedexclamationmarka-Deoxyguanosine5invertedexclamationmarka-(trihydrogendiphosphate), 2 inverted exclamation marka-Deoxyguanosine 5 inverted exclamation marka-(trihydrogen diphosphate)
- Molecular formula
- C10H15N5O10P2
- Empirical formula
- C10H15N5O10P2
- Molecular weight
- 427.2 g/mol
- Exact mass
- 427.02942
- CAS number
- 3493-09-2
- PubChem CID
- 135398595
- Canonical SMILES
- C1C(C(OC1N2C=NC3=C2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O)O
- Isomeric SMILES
- C1[C@@H]([C@H](O[C@H]1N2C=NC3=C2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O)O
- InChI
- InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
- InChIKey
- CIKGWCTVFSRMJU-KVQBGUIXSA-N
- Molfile
Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.
Calculated
- Heavy atoms
- 27
- Rings
- 3
- Aromatic rings
- 2
- Fraction sp³ carbons (Fsp3)
- 0.5
- H-bond donors
- 6
- H-bond acceptors
- 10 computed here · PubChem 12
- Rotatable bonds
- 6
- TPSA (Ų)
- 232.3 computed here · PubChem 228
- Formal charge
- 0
- XLogP3
- -4.5 PubChem
- Complexity
- 729 PubChem
- Stereocenters
- 3 defined, 1 undefinedCIP: C9: R · C11: S · C13: R · 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
- C28.12%
- H3.54%
- N16.39%
- O37.45%
- P14.50%
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)
- -1.44 ESOL (Delaney 2004), log mol/L
- Synthetic accessibility
- 4.21 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)
Drug-likeness: Lipinski’s rule of five
- Molecular weight ≤ 500: 427.2
- log P ≤ 5 (Crippen): -1.42
- 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: AiFChem, an XtalPi Company, CATO Research Chemicals Inc., 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) (positive) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Negative) · Human Metabolome Database (HMDB) (Positive)
- LC-MSMassBank Europe (Agilent 6530 Q-TOF LC/MS · LC-ESI-QTOF · NEGATIVE) · MassBank Europe (UPLC Q-Tof Premier, Waters · LC-ESI-QTOF · NEGATIVE) · MassBank of North America (MoNA) (UPLC Q-Tof Premier, Waters · LC-ESI-QTOF · ESI) · MassBank of North America (MoNA) (Q-Tof Premier, Waters · LC-Q-TOF/MS · ESI) · MassBank of North America (MoNA) (Thermo Q Exactive HF · LC-ESI-QFT · negative)
- 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]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.