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GDP-glucose

Athanor · official

C16H25N5O16P2 · 605.3 g/mol

IUPAC name: [[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] hydrogen phosphate

Also called GDP-Glc, glucosyl donor

CarbohydratesNucleic acid parts
Open in Athanor
The structure of GDP-glucose
Drawn from its SMILES with RDKit

Names and identifiers

IUPAC name
[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] hydrogen phosphate
Synonyms
GDP-Glc, glucosyl donor
Molecular formula
C16H25N5O16P2
Empirical formula
C16H25N5O16P2
Molecular weight
605.3 g/mol
Exact mass
605.07715
CAS number
10111-02-7
PubChem CID
136079130
Canonical SMILES
C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)N=C(NC2=O)N
Isomeric SMILES
C1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)N=C(NC2=O)N
InChI
InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11-,14-,15+/m1/s1
InChIKey
MVMSCBBUIHUTGJ-DFXODUROSA-N
Molfile

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

Calculated

Heavy atoms
39
Rings
4
Aromatic rings
2
Fraction sp³ carbons (Fsp3)
0.69
H-bond donors
10
H-bond acceptors
17 computed here · PubChem 18
Rotatable bonds
9
TPSA (Ų)
331.7 computed here · PubChem 327
Formal charge
0
XLogP3
-6.2 PubChem
Complexity
1050 PubChem
Stereocenters
9 defined, 2 undefinedCIP: C3: R · C5: S · P7: undefined · P11: undefined · C16: R · C18: R · C30: R · C32: S · C34: R · C36: S · C38: S
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

  • C31.75%
  • H4.16%
  • N11.57%
  • O42.29%
  • P10.23%

Isotope pattern

100%605.07720%606.0805.2%607.082608.084609.087

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
-4.63 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-0.25 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
4.99 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 605.34
  • log P ≤ 5 (Crippen): -4.63
  • H-bond donors ≤ 5: 10
  • H-bond acceptors ≤ 10: 17

Breaks 3 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.

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.