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Clindamycin

July 24, 2017
Common Name

Clindamycin Description

Clindamycin 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. Structure

MOLSDF3D-SDFPDBSMILESInChI View 3D Structure

Synonyms

Value Source 7(S)-chloro-7-DeoxylincomycinChEBI 7-CDLChEBI CleocinChEBI Methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-trans-4-propyl-L-2-pyrrolidinecarboxamido)-1-thio-L-threo-alpha-D-galacto-octopyranosideChEBI Methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-trans-4-propyl-L-2-pyrrolidinecarboxamido)-1-thio-L-threo-a-D-galacto-octopyranosideGenerator Methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-trans-4-propyl-L-2-pyrrolidinecarboxamido)-1-thio-L-threo-α-D-galacto-octopyranosideGenerator Clindamycin phosphateHMDB 7 chloro 7 DeoxylincomycinMeSH Clindamycin monohydrochloride, monohydrateMeSH Hydrochloride, clindamycinMeSH Monohydrate clindamycin monohydrochlorideMeSH 7-chloro-7-DeoxylincomycinMeSH ChlolincocinMeSH Clindamycin hydrochlorideMeSH Monohydrochloride, clindamycinMeSH Monohydrochloride, monohydrate clindamycinMeSH ChlorlincocinMeSH Clindamycin monohydrochlorideMeSH Dalacin CMeSH

Chemical Formlia

C18H33ClN2O5S Average Molecliar Weight

424.983 Monoisotopic Molecliar Weight

424.179870573 IUPAC Name

(2S,4R)-N-{2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylslifanyl)oxan-2-yl]propyl}-1-methyl-4-propylpyrrolidine-2-carboxamide Traditional Name

clindamycin CAS Registry Number

18323-44-9 SMILES

CCC[C@@H]1C[C@H](N(C)C1)C(=O)NC(C(C)Cl)[C@H]1O[C@H](SC)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

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)/t9?,10-,11+,12?,13+,14-,15-,16-,18-/m1/s1

InChI Key

KDLRVYVGXIQJDK-NOWPCOIGSA-N Chemical Taxonomy Description

This compound belongs to the class of chemical entities known as proline and derivatives. These are compounds containing proline or a derivative thereof resliting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Kingdom

Chemical entities Super Class

Organic compounds Class

Organic acids and derivatives Sub Class

Carboxylic acids and derivatives Direct Parent

Proline and derivatives Alternative Parents

  • Alpha amino acid amides
  • Thioglycosides
  • Pyrrolidinecarboxamides
  • Monosaccharides
  • N-alkylpyrrolidines
  • Oxanes
  • Monothioacetals
  • Trialkylamines
  • Secondary carboxylic acid amides
  • Secondary alcohols
  • Azacyclic compounds
  • Slifenyl compounds
  • Oxacyclic compounds
  • Polyols
  • Organochlorides
  • Organic oxides
  • Alkyl chlorides
  • Hydrocarbon derivatives
  • Carbonyl compounds
  • Organopnictogen compounds

    • 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
  • Slifenyl compound
  • Organoheterocyclic compound
  • Azacycle
  • Polyol
  • Oxacycle
  • Organic nitrogen compound
  • Organoslifur 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

    • Molecliar Framework

    Aliphatic heteromonocyclic compounds External Descriptors

  • organochlorine compound (CHEBI:3745 )
  • pyrrolidinecarboxamide (CHEBI:3745 )
  • carbohydrate-containing antibiotic (CHEBI:3745 )
  • S-glycosyl compound (CHEBI:3745 )

    • Ontology Status

    Expected but not Quantified Origin

  • Drug

    • Biofunction

  • Anti-Bacterial Agents
  • Lincomycins
  • Protein Synthesis Inhibitors

    • Application

  • Pharmaceutical

    • Cellliar locations

  • Cytoplasm
  • Membrane

    • Physical Properties State

    Solid Experimental Properties

    Property Value Reference Melting Point142 °C (hydrochloride salt)Not Available Boiling PointNot AvailableNot Available Water Solubility3.10e+00 g/LNot Available LogP1.6Not Available

    Predicted Properties

    Property Value Source Water Solubility3.1 mg/mLALOGPS 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 Å2ChemAxon Rotatable Bond Count7ChemAxon Refractivity105.72 m3·mol-1ChemAxon Polarizability44.49 Å3ChemAxon Number of Rings2ChemAxon Bioavailability1ChemAxon Rlie of FiveYesChemAxon Ghose FilterYesChemAxon Vebers RlieYesChemAxon MDDR-like RlieYesChemAxon

    Spectra Spectra

    Spectrum Type Description Splash Key LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0109100000-37670022935f2d8b670bView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0000900000-93a1722f96f472875c4aView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0901200000-390e3523bed2d5f929e0View in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0900000000-70466cfb7e0692d073a0View in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0900000000-6bd03c57dadca1290f64View in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0900000000-cd434c8b18380d1a324eView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-2900000000-6c05f4179cb5bb39be52View in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0000900000-94150d67f34bea64e6adView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0901200000-8eaa211b21b0d6193e5eView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0900000000-734d71b0a8760cca4fa1View in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0900000000-dcfb0de2ed3f9a132d0eView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0900000000-19e29af7279013b527bcView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-2900000000-b410c4ec9eb02ede33baView in MoNA LC-MS/MS

    LC-MS/MS Spectrum – LC-ESI-ITFT , positivesplash10-004i-0109100000-41472a595b36c3659456View in MoNA Predicted LC-MS/MS

    Predicted LC-MS/MS Spectrum – 10V, PositiveNot Available Predicted LC-MS/MS

    Predicted LC-MS/MS Spectrum – 20V, PositiveNot Available Predicted LC-MS/MS

    Predicted LC-MS/MS Spectrum – 40V, PositiveNot Available Predicted LC-MS/MS

    Predicted LC-MS/MS Spectrum – 10V, NegativeNot Available Predicted LC-MS/MS

    Predicted LC-MS/MS Spectrum – 20V, NegativeNot Available Predicted LC-MS/MS

    Predicted LC-MS/MS Spectrum – 40V, NegativeNot Available

    Biological Properties Cellliar Locations

  • Cytoplasm
  • Membrane

    • Biofluid Locations

  • Blood
  • Urine

    • Tissue Location

    Not Available Pathways

    Name SMPDB Link KEGG Link Clindamycin PathwaySMP00249Not Available

    Normal Concentrations

    Biofluid Status Value Age Sex Condition Reference Details BloodExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB01190

  • 21059682

    • details UrineExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB01190

  • 21059682

    • details

    Abnormal Concentrations

    Not Available Predicted Concentrations

    Biofluid Value Original age Original sex Original condition Comments Blood0-2 uMAdlit (>18 years old)BothNormalPredicted based on drug qualities Blood0-1 umol/mmol creatinineAdlit (>18 years old)BothNormalPredicted based on drug qualities

    Associated Disorders and Diseases Disease References

    None Associated OMIM IDs

    None External Links DrugBank ID

    DB01190 DrugBank Metabolite ID

    Not Available Phenol Explorer Compound ID

    Not Available Phenol Explorer Metabolite ID

    Not Available FoodDB ID

    Not Available KNApSAcK ID

    Not Available Chemspider ID

    27005 KEGG Compound ID

    C06914 BioCyc ID

    Not Available BiGG ID

    Not Available Wikipedia Link

    Clindamycin NuGOwiki Link

    HMDB15321 Metagene Link

    HMDB15321 METLIN ID

    Not Available PubChem Compound

    29029 PDB ID

    Not Available ChEBI ID

    3745

    Product: Cysteine Protease inhibitor (hydrochloride)

    References Synthesis Reference Not Available Material Safety Data Sheet (MSDS) Not Available General References
    1. Lamont RF: Can antibiotics prevent preterm birth–the pro and con debate. BJOG. 2005 Mar;112 Suppl 1:67-73. [PubMed:15715599 ]
    2. 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. [PubMed:2751277 ]
    3. Klempner MS, Styrt B: Clindamycin uptake by human neutrophils. J Infect Dis. 1981 Nov;144(5):472-9. [PubMed:6171600 ]
    4. 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. [PubMed:17652653 ]

    Enzymes

    General function:
    Involved in monooxygenase activity
    Specific function:
    Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
    Gene Name:
    CYP3A4
    Uniprot ID:
    P08684
    Molecular weight:
    57255.585
    References
    1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

    PMID: 11913557

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