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Database / Pharmaceutical impurity

Pharmaceutical impurity

Gentamicin C2

Gentamicin C2 is listed in the pharmaceutical impurity collection under CAS 25876-11-3. Its represented structure has formula C20H41N5O7 and a calculated molecular weight of 463.58 g/mol.

2D chemical structure

H N H O O H O O O H 2 N H 2 N H 2 N N H 2 O O H ( R ) ( R ) ( R ) ( S ) ( S ) ( R ) ( R ) ( S ) ( R ) ( R ) ( S ) ( R ) ( R )

Chemical identity

Catalog name
Gentamicin C2
Common name
Gentamicin C2
Chemical name
(2R,3R,4R,5R)-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,6S)-3-amino-6-[(1R)-1-aminoethyl]oxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol
CAS
25876-11-3
SMILES
CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H](O[C@H]3O[C@H]([C@@H](C)N)CC[C@H]3N)[C@@H](N)C[C@H]2N)OC[C@]1(C)O
InChI
InChI=1S/C20H41N5O7/c1-8(21)12-5-4-9(22)18(30-12)31-15-10(23)6-11(24)16(13(15)26)32-19-14(27)17(25-3)20(2,28)7-29-19/h8-19,25-28H,4-7,21-24H2,1-3H3/t8-,9-,10+,11-,12+,13+,14-,15-,16+,17-,18-,19-,20+/m1/s1
InChIKey
XUFIWSHGXVLULG-IDLVJFIQSA-N

Record ID: A1280237809c3

Computed properties

C20H41N5O7 Molecular formula
463.576 g/molMolecular weight
463.3006 DaMonoisotopic exact mass
213.72 ŲTopological polar surface area
-3.5882 Calculated LogP (Wildman–Crippen)
115.0587 cm³/molMolar refractivity (Wildman–Crippen)
12 countHydrogen-bond acceptors
8 countHydrogen-bond donors

Descriptors are calculated from the displayed SMILES. Calculated LogP is not a measured partition coefficient or a pH-specific LogD.

Molecular descriptor profile

Descriptor radar

Mol. weight LogP TPSA HBA HBD Rotatable 25 50 75 100

Structural feature counts

0 4 8 12 Count H-bond acceptors H-bond donors Rotatable bonds Rings Aromatic rings Stereo centers

Element composition

C H N O 0 10 20 30 40 Number of atoms

Radar scale: 0–100 percentile within 25,771 distinct represented structures in this release, using the midpoint rank for ties. Larger values indicate a higher descriptor rank, not greater safety or toxicity. Element counts include hydrogen and combine isotopes under each element.

Radar values and percentile reference
DescriptorValuePercentile
Molecular weight463.57680.86
Calculated LogP (Wildman–Crippen)-3.58821.93
Topological polar surface area213.7296.20
Hydrogen-bond acceptors1295.82
Hydrogen-bond donors898.12
Rotatable bonds (strict)669.73

Complete molecular descriptors

PropertyCalculated valueUnit / type
Molecular formulaC20H41N5O7dimensionless
Molecular weight463.576g/mol
Monoisotopic exact mass463.3006Da
Topological polar surface area213.72Ų
Calculated LogP (Wildman–Crippen)-3.5882dimensionless
Molar refractivity (Wildman–Crippen)115.0587cm³/mol
Hydrogen-bond acceptors12count
Hydrogen-bond donors8count
Rotatable bonds (strict)6count
Heavy atoms32count
Heteroatoms12count
Rings3count
Aromatic rings0count
Aliphatic rings3count
Saturated rings3count
Aromatic heterocycles0count
Aliphatic heterocycles2count
Saturated heterocycles2count
Aromatic carbocycles0count
Aliphatic carbocycles1count
Fraction of sp³ carbon atoms1fraction
Formal charge0e
Disconnected components1count
Isotopically specified atoms0count
Potential atom stereocenters13count
Unspecified atom stereocenters0count
Spiro atoms0count
Bridgehead atoms0count
Labute approximate surface area188.402Ų
Valence electrons188count
Radical electrons0count
Bertz complexity614.8877index
Balaban J1.688index

Ring categories overlap and should not be summed. No toxicity result, PDE, HBEL or acceptable intake is inferred from these descriptors.

Toxicological services and resources for Gentamicin C2

Qualification and safety assessment of Gentamicin C2

Explore toxicological qualification of Gentamicin C2 and ICH M7 mutagenic impurity assessment of Gentamicin C2 for evaluation of this impurity in its pharmaceutical context.

Where data gaps need to be addressed, resources include read-across assessment for Gentamicin C2 and acceptable intake and limit justification for Gentamicin C2. The relevant approach depends on the available evidence, exposure and duration of use.

Related Altox services and technical resources

Identity sources and calculation method

Identifiers originate from the source catalogues and available public identity records. InChI and InChIKey on this page are generated from the displayed SMILES. RDKit validation checks the molecular representation; it does not independently verify every catalogue assignment.

Discuss an assessment for Gentamicin C2

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