Clindamycin
Athanor · official
C18H33ClN2O5S · 425 g/mol
IUPAC name: N-[2-chloro-1-(3,4,5-trihydroxy-6-methylsulfanyloxan-2-yl)propyl]-1-methyl-4-propylpyrrolidine-2-carboxamide
Also called Cleocin, Dalacin, lincosamide
Names and identifiers
- IUPAC name
- N-[2-chloro-1-(3,4,5-trihydroxy-6-methylsulfanyloxan-2-yl)propyl]-1-methyl-4-propylpyrrolidine-2-carboxamide
- Synonyms
- Cleocin, Dalacin, lincosamide
+ 35 more
DTXSID70860219, methyl 7-chloro-6,7,8-trideoxy-6-[(1-methyl-4-propylprolyl)amino]-1-thiooctopyranoside, Methyl 7-chloro-6,7,8-trideoxy-6-((1-methyl-4-propylprolyl)amino)-1-thiooctopyranoside, RefChem:1089516, DTXCID00197040, N-{2-chloro-1-[3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl}-1-methyl-4-propylpyrrolidine-2-carboxamide, MLS001183714, N-(2-Chloro-1-(3,4,5-trihydroxy-6-(methylthio)tetrahydro-2H-pyran-2-yl)propyl)-1-methyl-4-propylpyrrolidine-2-carboxamide, Klimicin, ClindaDerm, Klindan 300, SMR000677917, MLS006011824, CHEMBL10766, SCHEMBL12356681, CHEBI:95137, KDLRVYVGXIQJDK-UHFFFAOYSA-N, HMS2231K05, HMS3372M13, HMS3651N15, HMS5081B19, l-threo-.alpha.-d-Galacto-octopyranoside, methyl 7-chloro-6,7,8-trideoxy-6-[[(1-methyl-4-propyl-2-pyrrolidinyl)carbonyl]amino]-1-thio-, (2S-trans)-, Methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-trans-4-propyl-L-2-pyrrolidinecarboxamido)-1-thio-L-threo-.alpha.-D-galacto-octopyranoside, BBL005238, s2830, STK177246, AKOS005410727, N-[2-chloro-1-(3,4,5-trihydroxy-6-methylsulfanyloxan-2-yl)propyl]-1-methyl-4-propylpyrrolidine-2-carboxamide, N-[2-chloro-1-[3,4,5-trihydroxy-6-(methylthio)-2-oxanyl]propyl]-1-methyl-4-propyl-2-pyrrolidinecarboxamide, DB-044486, CS-0291705, NS00077368, EN300-51913, Q27166924, L-threo-d-Galacto-octopyranoside, methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-4-propyl-l-2-pyrrolidinecarboxamido)-1-thio-, trans- .alpha.-
- Molecular formula
- C18H33ClN2O5S
- Empirical formula
- C18H33ClN2O5S
- Molecular weight
- 425 g/mol
- Exact mass
- 424.17987
- CAS number
- 18323-44-9
- PubChem CID
- 2786
- Canonical SMILES
- CCCC1CC(N(C1)C)C(=O)NC(C2C(C(C(C(O2)SC)O)O)O)C(C)Cl
- Isomeric SMILES
- CCCC1CC(N(C1)C)C(=O)NC(C2C(C(C(C(O2)SC)O)O)O)C(C)Cl
- InChI
- InChI=1S/C18H33ClN2O5S/c1-5-6-10-7-11(21(3)8-10)17(25)20-12(9(2)19)16-14(23)13(22)15(24)18(26-16)27-4/h9-16,18,22-24H,5-8H2,1-4H3,(H,20,25)
- InChIKey
- KDLRVYVGXIQJDK-UHFFFAOYSA-N
- Molfile
Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.
Calculated
- Heavy atoms
- 27
- Rings
- 2
- Aromatic rings
- 0
- Fraction sp³ carbons (Fsp3)
- 0.94
- H-bond donors
- 4
- H-bond acceptors
- 7
- Rotatable bonds
- 7
- TPSA (Ų)
- 102.3 computed here · PubChem 128
- Formal charge
- 0
- XLogP3
- 2.2 PubChem
- Complexity
- 502 PubChem
- Stereocenters
- 0 defined, 9 undefinedCIP: C4: undefined · C6: undefined · C10: undefined · C11: undefined · C14: undefined · C16: undefined · C19: undefined · C21: undefined · C23: 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
- C50.87%
- H7.83%
- Cl8.34%
- N6.59%
- O18.82%
- S7.55%
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
- 0.39 Crippen (Wildman and Crippen 1999)
- log S (water solubility)
- -2.26 ESOL (Delaney 2004), log mol/L
- Synthetic accessibility
- 4.74 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)
Drug-likeness: Lipinski’s rule of five
- Molecular weight ≤ 500: 424.99
- log P ≤ 5 (Crippen): 0.39
- 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
No GHS hazard classification was found in the sources.
Safety data sheets on the supplier’s page: Enamine, BOC Sciences, Ambinter.
Always read the supplier’s safety data sheet before working with it.
Spectra
- 13C NMRSpectraBase
- GC-MSNIST Mass Spectrometry Data Center · NIST Mass Spectrometry Data Center · SpectraBase (GC/MS)
- MS-MSNIST Mass Spectrometry Data Center (IT/ion trap) · NIST Mass Spectrometry Data Center (IT/ion trap)
- LC-MSMassBank Europe (TripleTOF 5600 SCIEX · LC-ESI-QTOF · POSITIVE) · MassBank Europe (TripleTOF 5600 SCIEX · LC-ESI-QTOF · POSITIVE) · MassBank Europe (TripleTOF 5600 SCIEX · LC-ESI-QTOF · POSITIVE) · MassBank Europe (TripleTOF 5600 SCIEX · LC-ESI-QTOF · POSITIVE) · MassBank Europe (TripleTOF 5600 SCIEX · LC-ESI-QTOF · POSITIVE) · MassBank Europe (TripleTOF 5600 SCIEX · LC-ESI-QTOF · POSITIVE)
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]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
- [2]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
- [3]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
- [4]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.