Ganciclovir (C9H13N5O4): structure, properties and hazards

Names and identifiers

IUPAC name: 2-amino-9-(1,3-dihydroxypropan-2-yloxymethyl)-1H-purin-6-one
Synonyms: Cytovene, CMV, Gancyclovir
+ 37 more
Vitrasert, Zirgan, BW-759U, Ganciclovirum, RS-21592, BW 759U, Cymevene, Virgan, Cymevan, 2'-Nor-2'-deoxyguanosine, 9-((2-Hydroxy-1-(hydroxymethyl)ethoxy)methyl)guanine, 9-[(1,3-Dihydroxy-2-propoxy)methyl]guanine, DTXSID8041032, P9G3CKZ4P5, 9-((1,3-Dihydroxy-2-propoxy)methyl)guanine, NSC-759656, 2-amino-9-{[(1,3-dihydroxypropan-2-yl)oxy]methyl}-6,9-dihydro-3H-purin-6-one, 2-amino-9-(1,3-dihydroxypropan-2-yloxymethyl)-1H-purin-6-one, CHEBI:465284, 2-(6-Amino-purin-9-ylmethoxy)-propane-1,3-diol, 2-amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-1H-purin-6(9H)-one, 6H-Purin-6-one, 2-amino-1,9-dihydro-9-((2-hydroxy-1-(hydroxymethyl)ethoxy)methyl)-, DTXCID6021032, 2-amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-9H-purin-6-ol, 2-amino-9-(1,3-dihydroxypropan-2-yloxymethyl)-3H-purin-6-one, 2-amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-3H-purin-6(9H)-one, 2-Amino-9-(2-hydroxy-1-hydroxymethyl-ethoxymethyl)-1,9-dihydro-purin-6-one, 2-amino-9-(2-hydroxy-1-hydroxymethylethoxymethyl)-6,9-dihydro-1H-6-purinone, 9-[[2-Hydroxy-1-(hydroxymethyl)ethoxy]methyl]guanine, Nordeoxyguanosine, NSC716361, Ganzyk-rtu, 2-amino-9-(((1,3-dihydroxypropan-2-yl)oxy)methyl)-6,9-dihydro-3H-purin-6-one, RefChem:922069, 2'NDG, Ganciclovir, Monosodium Salt, J05AB06
Molecular formula: C₉H₁₃N₅O₄
Empirical formula: C₉H₁₃N₅O₄
Molecular weight: 255.23 g/mol
Exact mass: 255.09675
CAS number: 82410-32-0
PubChem CID: 135398740
Canonical SMILES: C1=NC2=C(N1COC(CO)CO)N=C(NC2=O)N
Isomeric SMILES: C1=NC2=C(N1COC(CO)CO)N=C(NC2=O)N
InChI: InChI=1S/C9H13N5O4/c10-9-12-7-6(8(17)13-9)11-3-14(7)4-18-5(1-15)2-16/h3,5,15-16H,1-2,4H2,(H3,10,12,13,17)
InChIKey: IRSCQMHQWWYFCW-UHFFFAOYSA-N
Molfile

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

Physical properties

Appearance: White to off-white solid[1]
Solubility in water: Aqueous solubility of the drug is relatively constant over a pH range of 3.5-8.5 but increases substantially in strongly acidic or basic solutions.[1]
2 values
From Hazardous Substances Data Bank (HSDB), the most authoritative source here.
Value As written Source
– Ganciclovir sodium sterile powder occurs as a white to off-white, crystalline, lyophilized powder. Ganciclovir sodium has a solubility of 3 mg/mL in water at 25 °C and neutral pH. Both ganciclovir base and ganciclovir sodium are freely soluble in water at high pH (around 11). At more neutral pH, solubility is reduced, and crystallization may occur in concentrated solutions of the drug (exceeding 10 mg/ml). Ganciclovir sodium contains approximately 4 mEq of sodium per gram of ganciclovir. Following reconstitution with sterile water for injection, ganciclovir sodium solutions containing 50 mg of [1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386
–shown Aqueous solubility of the drug is relatively constant over a pH range of 3.5-8.5 but increases substantially in strongly acidic or basic solutions. [1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386
log P: log Kow = -1.66[1]
pKa: pKa1 2.2[1]
2 values
Only one source reports it.
Value As written Source
–shown pKa1 2.2 [1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386
– pKa2 9.4 [1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386

Value	As written	Source
–	Ganciclovir sodium sterile powder occurs as a white to off-white, crystalline, lyophilized powder. Ganciclovir sodium has a solubility of 3 mg/mL in water at 25 °C and neutral pH. Both ganciclovir base and ganciclovir sodium are freely soluble in water at high pH (around 11). At more neutral pH, solubility is reduced, and crystallization may occur in concentrated solutions of the drug (exceeding 10 mg/ml). Ganciclovir sodium contains approximately 4 mEq of sodium per gram of ganciclovir. Following reconstitution with sterile water for injection, ganciclovir sodium solutions containing 50 mg of	[1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386
–shown	Aqueous solubility of the drug is relatively constant over a pH range of 3.5-8.5 but increases substantially in strongly acidic or basic solutions.	[1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386

Value	As written	Source
–shown	pKa1 2.2	[1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386
–	pKa2 9.4	[1] Hazardous Substances Data Bank (HSDB)cites McEvoy, G.K. (ed.). American Hospital Formulary Service - Drug Information 93. Bethesda, MD: American Society of Hospital Pharmacists, Inc., 1993 (Plus Supplements, 1993)., p. 386

Each value as its source reports it, with the source's number after it (listed under References). Where several sources report a property, the row shows the value most of them agree on, the rule the app uses; open the values to see every one.

Calculated

Heavy atoms: 18
Rings: 2
Aromatic rings: 2
Fraction sp³ carbons (Fsp3): 0.44
H-bond donors: 4
H-bond acceptors: 7 computed here · PubChem 6
Rotatable bonds: 5
TPSA (Å²): 139.3 computed here · PubChem 135
Formal charge: 0
XLogP3: -2.5 PubChem
Complexity: 346 PubChem
Stereocenters: None
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

C42.35%
H5.13%
N27.44%
O25.07%

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: -1.97 Crippen (Wildman and Crippen 1999)
log S (water solubility): -0.22 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 3 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 255.23
log P ≤ 5 (Crippen): -1.97
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

Danger

Most widely reported: 46 company reports to ECHA. Source [2].

Health hazard

H360May damage fertility or the unborn child (93.5% of reports)

Precautionary statements: P203, P280, P318, P405, P501

Storage

Keep container tightly closed in a dry and well-ventilated place. Recommended storage temperature: 2 - 8 °C. Keep in a dry place.[1]
Ganciclovir capsules should be stored at 5-25 °C and ganciclovir sodium sterile powder should be stored at room temperature; exposure to temperatures exceeding 40 °C should be avoided.[1]

Safety data sheets on the supplier’s page: Selleck Chemicals, Vitas-M Laboratory, Alfa Chemistry.

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]Hazardous Substances Data Bank (HSDB) · Public domain (US NLM) · via PubChem · retrieved 2026-10-14
[2]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[3]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[4]Human Metabolome Database (HMDB) · 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%.