Clindamycin (T3D3497)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationXML
Record Information
Version2.0
Creation Date2009-07-30 17:58:48 UTC
Update Date2014-12-24 20:26:07 UTC
Accession NumberT3D3497
Identification
Common NameClindamycin
ClassSmall Molecule
DescriptionClindamycin is a semisynthetic lincosamide antibiotic that has largely replaced lincomycin due to an improved side effect profile. Clindamycin inhibits bacterial protein synthesis by binding to bacterial 50S ribosomal subunits. It may be bacteriostatic or bactericidal depending on the organism and drug concentration.
Compound Type
  • Amide
  • Amine
  • Anti-Bacterial Agent
  • Antibiotic
  • Drug
  • Ether
  • Lincomycin
  • Metabolite
  • Organic Compound
  • Organochloride
  • Protein Synthesis Inhibitor
  • Synthetic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
7(S)-Chloro-7-deoxylincomycin
7-CDL
Cleocin
Clinda-Derm
Clindagel
Clindamax
Clindamicina
Clindamycin Phosphate
Clindamycine
Clindamycinum
Clindesse
Clindets
Clinimycin
Dalacin C
Dalacin T Topical Solution
Evoclin
Methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-trans-4-propyl-L-2-pyrrolidinecarboxamido)-1-thio-L-threo-alpha-D-galacto-octopyranoside
Zindaclin
Chemical FormulaC18H33ClN2O5S
Average Molecular Mass424.983 g/mol
Monoisotopic Mass424.180 g/mol
CAS Registry Number18323-44-9
IUPAC Name(2S,4R)-N-{2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl}-1-methyl-4-propylpyrrolidine-2-carboxamide
Traditional Nameclindamycin
SMILES[H]C(C)(Cl)C([H])(N=C(O)[C@]1([H])C[C@@]([H])(CCC)CN1C)[C@@]1([H])O[C@]([H])(SC)[C@]([H])(O)[C@@]([H])(O)[C@@]1([H])O
InChI IdentifierInChI=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)/t9?,10-,11+,12?,13+,14-,15-,16-,18-/m1/s1
InChI KeyInChIKey=KDLRVYVGXIQJDK-NOWPCOIGSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentProline and derivatives
Alternative Parents
Substituents
  • Proline or derivatives
  • Alpha-amino acid amide
  • Glycosyl compound
  • S-glycosyl compound
  • Pyrrolidine carboxylic acid or derivatives
  • Pyrrolidine-2-carboxamide
  • Monosaccharide
  • Oxane
  • N-alkylpyrrolidine
  • Monothioacetal
  • Pyrrolidine
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Tertiary amine
  • Tertiary aliphatic amine
  • Sulfenyl compound
  • Organoheterocyclic compound
  • Azacycle
  • Polyol
  • Oxacycle
  • Organic nitrogen compound
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Alkyl chloride
  • Alcohol
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Organopnictogen compound
  • Organic oxide
  • Alkyl halide
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
Pathways
NameSMPDB LinkKEGG Link
Clindamycin PathwayNot AvailableNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting Point142 [HCl salt]
Boiling PointNot Available
Solubility30.6 mg/L
LogP2.16
Predicted Properties
PropertyValueSource
Water Solubility3.1 g/LALOGPS
logP1.76ALOGPS
logP1.04ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)12.16ChemAxon
pKa (Strongest Basic)7.55ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area102.26 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity105.72 m³·mol⁻¹ChemAxon
Polarizability44.49 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9834100000-dda83549a397e87777582017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-004i-9821028000-cf121bc5f21859a54a2d2017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0109100000-37670022935f2d8b670b2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0000900000-93a1722f96f472875c4a2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0901200000-390e3523bed2d5f929e02017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-70466cfb7e0692d073a02017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-6bd03c57dadca1290f642017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-cd434c8b18380d1a324e2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-2900000000-6c05f4179cb5bb39be522017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0000900000-94150d67f34bea64e6ad2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0901200000-8eaa211b21b0d6193e5e2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-734d71b0a8760cca4fa12017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-dcfb0de2ed3f9a132d0e2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-19e29af7279013b527bc2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-2900000000-b410c4ec9eb02ede33ba2017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0109100000-41472a595b36c36594562017-09-14View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-004i-0901200000-3314779cf85f40a0e6882021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-004i-0901200000-d615b9b4b52a5859a63c2021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 15V, Positivesplash10-004i-0000900000-93a1722f96f472875c4a2021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 60V, Positivesplash10-004i-0900000000-b712dc39bbf605193fb42021-09-20View Spectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0109100000-9de33a60fefa24d804902021-09-20View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00b9-0252900000-2254bf9c796a153450b92016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2940000000-1fdb89b36ba4c00702a92016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-3d2d9fcc4ca24ef1ed7e2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fka-9456300000-91a0536cf229efc7485e2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000b-9312100000-7aa19239c8a21976d0de2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kg-9610000000-4db0493cafa43fc798942016-08-03View Spectrum
Toxicity Profile
Route of ExposureOral; topical; parenteral (intramuscular, intravenous). Rapidly absorbed after oral administration with peak serum concentrations observed after about 45 minutes. Absorption of an oral dose is virtually complete (90%) and the concomitant intake of food does not appreciably modify the serum concentrations; serum levels have been uniform and predictable from person to person and dose to dose. Clindamycin does not penetrate the blood brain barrier.
Mechanism of ToxicitySystemic/vaginal clindamycin inhibits protein synthesis of bacteria by binding to the 50S ribosomal subunits of the bacteria. Specifically, it binds primarily to the 23s RNA subunit. Topical clindamycin reduces free fatty acid concentrations on the skin and suppresses the growth of Propionibacterium acnes (Corynebacterium acnes) , an anaerobe found in sebaceous glands and follicles.
MetabolismHepatic Route of Elimination: Approximately 10% of the bioactivity is excreted in the urine and 3.6% in the feces; the remainder is excreted as bioinactive metabolites. Half Life: 2.4 hours
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesUsed to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria. It is a common topical treatment for acne and can be useful against some methicillin-resistant Staphylococcus aureus (MRSA) infections. [Wikipedia] For the treatment of serious infections caused by susceptible anaerobic bacteria, including Bacteroides spp., Peptostreptococcus, anaerobic streptococci, Clostridium spp., and microaerophilic streptococci. May be useful in polymicrobic infections such as intra-abdominal or pelvic infections, osteomyelitis, diabetic foot ulcers, aspiration pneumonia and dental infections. May also be used to treat MSSA and respiratory infections caused by S. pneumoniae and S. pyogenes in patients who are intolerant to other indicated antibiotics or who are infected with resistant organism. May be used vaginally to treat vaginosis caused by Gardnerella vaginosa. Clindamycin reduces the toxin producing effects of S. aureus and S. pyogenes and as such, may be particularly useful for treating necrotizing fasciitis. May be used topically to treat acne.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsOrally and parenterally administered clindamycin has been associated with severe colitis (pseudomembranous colitis) which may result in patient death. Use of the topical formulation of clindamycin results in absorption of the antibiotic from the skin surface. Diarrhea, bloody diarrhea, and colitis (including pseudomembranous colitis) have been reported with the use of topical and systemic clindamycin.
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB01190
HMDB IDHMDB15321
PubChem Compound ID29029
ChEMBL IDCHEMBL2303635
ChemSpider ID27005
KEGG IDC06914
UniProt IDNot Available
OMIM ID
ChEBI ID3745
BioCyc IDNot Available
CTD IDNot Available
Stitch IDClindamycin
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkClindamycin
References
Synthesis Reference

Donald E. Ayer, Carl A. Schlagel, Gordon L. Flynn, “Topical clindamycin preparations.” U.S. Patent US4018918, issued January, 1971.

MSDSLink
General References
  1. Daum RS: Clinical practice. Skin and soft-tissue infections caused by methicillin-resistant Staphylococcus aureus. N Engl J Med. 2007 Jul 26;357(4):380-90. [17652653 ]
  2. Klempner MS, Styrt B: Clindamycin uptake by human neutrophils. J Infect Dis. 1981 Nov;144(5):472-9. [6171600 ]
  3. Lamont RF: Can antibiotics prevent preterm birth--the pro and con debate. BJOG. 2005 Mar;112 Suppl 1:67-73. [15715599 ]
  4. Plaisance KI, Drusano GL, Forrest A, Townsend RJ, Standiford HC: Pharmacokinetic evaluation of two dosage regimens of clindamycin phosphate. Antimicrob Agents Chemother. 1989 May;33(5):618-20. [2751277 ]
  5. Drugs.com [Link]
Gene Regulation
Up-Regulated Genes
GeneGene SymbolGene IDInteractionChromosomeDetails
Down-Regulated GenesNot Available