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Record Information
Version3.6
Creation Date2012-09-06 15:16:51 UTC
Update Date2016-02-11 01:32:24 UTC
HMDB IDHMDB15321
Secondary Accession NumbersNone
Metabolite Identification
Common NameClindamycin
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.
Structure
Thumb
Synonyms
ValueSource
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
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
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 KeyInChIKey=KDLRVYVGXIQJDK-NOWPCOIGSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acid amides
Alternative Parents
Substituents
  • Alpha-amino acid amide
  • S-glycosyl compound
  • Glycosyl compound
  • Pyrrolidine-2-carboxamide
  • Pyrrolidine carboxylic acid or derivatives
  • N-alkylpyrrolidine
  • Oxane
  • Monosaccharide
  • Saccharide
  • Pyrrolidine
  • Monothioacetal
  • Tertiary aliphatic amine
  • Tertiary amine
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Polyol
  • Carboxamide group
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Sulfenyl compound
  • Thioether
  • Carboxylic acid amide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Carbonyl group
  • Amine
  • Alkyl halide
  • Alkyl chloride
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Drug
Biofunction
  • Anti-Bacterial Agents
  • Lincomycins
  • Protein Synthesis Inhibitors
Application
  • Pharmaceutical
Cellular locations
  • Cytoplasm
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point142 °C (hydrochloride salt)Not Available
Boiling PointNot AvailableNot Available
Water Solubility3.10e+00 g/LNot Available
LogP1.6Not Available
Predicted Properties
PropertyValueSource
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
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Clindamycin PathwaySMP00249Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01190
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01190
  • Not Applicable
details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiofluidValueOriginal ageOriginal sexOriginal conditionComments
Blood0-2 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0-1 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01190
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID27005
KEGG Compound IDC06914
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkClindamycin
NuGOwiki LinkHMDB15321
Metagene LinkHMDB15321
METLIN IDNot Available
PubChem Compound29029
PDB IDNot Available
ChEBI ID3745
References
Synthesis ReferenceNot 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. [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. [2751277 ]
  3. Klempner MS, Styrt B: Clindamycin uptake by human neutrophils. J Infect Dis. 1981 Nov;144(5):472-9. [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. [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. Epub 2009 Nov 24. [19934256 ]