Clarithromycin (C38H69NO13): structure, properties and hazards

Names and identifiers

IUPAC name: (3R,4S,5S,6R,7R,9R,11R,12R,13S,14R)-6-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-14-ethyl-12,13-dihydroxy-4-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-7-methoxy-3,5,7,9,11,13-hexamethyl-oxacyclotetradecane-2,10-dione
Synonyms: Biaxin, macrolide, 6-O-Methylerythromycin
+ 36 more
Klaricid, Clarithromycine, Erythromycin, 6-O-methyl-, 6-O-Methylerythromycin a, Macladin, Klacid, Veclam, Abbott-56268, Zeclar, Mavid, Naxy, Claritromicina, Cyllind, Clarithromycinum, TE-031, Biaxin XL, A-56268, DTXSID3022829, Clarithromycin identity, Clarosip, Klaricid XL, TE031, Clarithromycin extended release, NSC-758704, H1250JIK0A, DTXCID40820062, CHEBI:3732, (3R,4S,5S,6R,7R,9R,11R,12R,13S,14R)-6-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-14-ethyl-12,13-dihydroxy-4-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-7-methoxy-3,5,7,9,11,13-hexamethyl-oxacyclotetradecane-2,10-dione, A56268, Clarithromycin [USAN:USP:INN:BAN:JAN], Clarithromycin (USAN:USP:INN:BAN:JAN), Klaricid adult, Klaricid paed, Mycifor xl, Xetinin xl, Clarie xl
Molecular formula: C₃₈H₆₉NO₁₃
Empirical formula: C₃₈H₆₉NO₁₃
Molecular weight: 748 g/mol
Exact mass: 747.47689
CAS number: 81103-11-9
PubChem CID: 84029
Canonical SMILES: CCC1C(C(C(C(=O)C(CC(C(C(C(C(C(=O)O1)C)OC2CC(C(C(O2)C)O)(C)OC)C)OC3C(C(CC(O3)C)N(C)C)O)(C)OC)C)C)O)(C)O
Isomeric SMILES: CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)OC)C)C)O)(C)O
InChI: InChI=1S/C38H69NO13/c1-15-26-38(10,45)31(42)21(4)28(40)19(2)17-37(9,47-14)33(52-35-29(41)25(39(11)12)16-20(3)48-35)22(5)30(23(6)34(44)50-26)51-27-18-36(8,46-13)32(43)24(7)49-27/h19-27,29-33,35,41-43,45H,15-18H2,1-14H3/t19-,20-,21+,22+,23-,24+,25+,26-,27+,29-,30+,31-,32+,33-,35+,36-,37-,38-/m1/s1
InChIKey: AGOYDEPGAOXOCK-KCBOHYOISA-N
Molfile

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

Physical properties

log P: log Kow = 3.16[1]
pKa: pKa = 8.99[1]

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: 52
Rings: 3
Aromatic rings: 0
Fraction sp³ carbons (Fsp3): 0.95
H-bond donors: 4
H-bond acceptors: 14
Rotatable bonds: 8
TPSA (Å²): 182.9 computed here · PubChem 183
Formal charge: 0
XLogP3: 3.2 PubChem
Complexity: 1190 PubChem
Stereocenters: 0 defined, 18 undefinedCIP: C3: undefined · C7: undefined · C9: undefined · C11: undefined · C13: undefined · C17: undefined · C19: undefined · C22: undefined · C24: undefined · C26: undefined · C28: undefined · C31: 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

C61.02%
H9.30%
N1.87%
O27.81%

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: 2.44 Crippen (Wildman and Crippen 1999)
log S (water solubility): -5.49 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 6.24 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 747.96
log P ≤ 5 (Crippen): 2.44
H-bond donors ≤ 5: 4
H-bond acceptors ≤ 10: 14

Breaks 2 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

Warning

Most widely reported: 243 company reports to ECHA. Source [2].

Harmful or irritant

H302Harmful if swallowed (99.2% of reports)

Precautionary statements: P264, P270, P301+P317, P330, P501

View all classifications (2)

[2] European Chemicals Agency (ECHA) · 243 reports · WarningH302
[2] European Chemicals Agency (ECHA) · WarningH302, H315, H361d, H373, H400

Storage

Store in tight container as defined in the usp-nf. This material should be handled and stored per label instructions to ensure product integrity.[1]
Clarithromycin granules for oral suspension should be stored in well-closed containers at 15-30 °C. Following reconstitution as directed, oral suspensions of clarithromycin should be stored at 15-30 °C in well-closed containers; the reconstituted suspension should not be refrigerated.[1]
Commercially available clarithromycin 250-mg conventional tablets should be stored in well-closed containers at 15-30 °C and should be protected from light.1 Clarithromycin 500-mg conventional tablets should be stored in well- closed containers at controlled room temperature between 20-25 det C. Clarithromycin extended-release tablets should be stored at 20-25 °C, but may be exposed to temperatures ranging from 15-30 °C.[1]

Safety data sheets on the supplier’s page: LGC Standards, AppChem, CATO Research Chemicals Inc..

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%.