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Record Information
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2020-02-26 21:41:23 UTC
Secondary Accession Numbers
  • HMDB15321
Metabolite Identification
Common NameClindamycin
DescriptionClindamycin, also known as cleocin or 7-CDL, 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. Clindamycin is a drug. Clindamycin is a semisynthetic lincosamide antibiotic that has largely replaced lincomycin due to an improved side effect profile. Clindamycin is a very strong basic compound (based on its pKa). In humans, clindamycin is involved in clindamycin action pathway. Orally 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. Clindamycin is a potentially toxic compound. Rapidly absorbed after oral administration with peak serum concentrations observed after about 45 minutes. Oral; topical; parenteral (intramuscular, intravenous). Systemic/vaginal clindamycin inhibits protein synthesis of bacteria by binding to the 50S ribosomal subunits of the bacteria.
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 deoxylincomycinHMDB
Clindamycin monohydrochloride, monohydrateHMDB
Hydrochloride, clindamycinHMDB
Monohydrate clindamycin monohydrochlorideHMDB
Clindamycin hydrochlorideHMDB
Monohydrochloride, clindamycinHMDB
Monohydrochloride, monohydrate clindamycinHMDB
Clindamycin monohydrochlorideHMDB
Dalacin CHMDB
Chemical FormulaC18H33ClN2O5S
Average Molecular Weight424.983
Monoisotopic Molecular Weight424.179870573
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
CAS Registry Number18323-44-9
InChI Identifier
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
  • 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
Physiological effect

Health effect:



Route of exposure:

Biological location:


Naturally occurring process:


Environmental role:

Biological role:

Industrial application:

Physical Properties
Experimental Properties
Melting Point142 °C (hydrochloride salt)Not Available
Boiling PointNot AvailableNot Available
Water Solubility3.1 g/LNot Available
LogP1.6Not Available
Predicted Properties
Water Solubility3.1 g/LALOGPS
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
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9834100000-dda83549a397e8777758Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-004i-9821028000-cf121bc5f21859a54a2dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0109100000-37670022935f2d8b670bSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0000900000-93a1722f96f472875c4aSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0901200000-390e3523bed2d5f929e0Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-70466cfb7e0692d073a0Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-6bd03c57dadca1290f64Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-cd434c8b18380d1a324eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-2900000000-6c05f4179cb5bb39be52Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0000900000-94150d67f34bea64e6adSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0901200000-8eaa211b21b0d6193e5eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-734d71b0a8760cca4fa1Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-dcfb0de2ed3f9a132d0eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0900000000-19e29af7279013b527bcSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-2900000000-b410c4ec9eb02ede33baSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-004i-0109100000-41472a595b36c3659456Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00b9-0252900000-2254bf9c796a153450b9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2940000000-1fdb89b36ba4c00702a9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-3d2d9fcc4ca24ef1ed7eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fka-9456300000-91a0536cf229efc7485eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000b-9312100000-7aa19239c8a21976d0deSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kg-9610000000-4db0493cafa43fc79894Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Normal Concentrations
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01190 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01190 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01190
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID27005
KEGG Compound IDC06914
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkClindamycin
METLIN IDNot Available
PubChem Compound29029
PDB IDNot Available
ChEBI ID3745
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. Klempner MS, Styrt B: Clindamycin uptake by human neutrophils. J Infect Dis. 1981 Nov;144(5):472-9. [PubMed:6171600 ]
  3. Lamont RF: Can antibiotics prevent preterm birth--the pro and con debate. BJOG. 2005 Mar;112 Suppl 1:67-73. [PubMed:15715599 ]
  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 ]


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:
Uniprot ID:
Molecular weight:
  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 ]