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Record Information
Version4.0
Creation Date2012-09-06 15:16:51 UTC
Update Date2017-09-25 12:22:27 UTC
HMDB IDHMDB0015342
Secondary Accession Numbers
  • HMDB15342
StatusExpected but not Quantified
Metabolite Identification
Common NameClarithromycin
DescriptionClarithromycin, a semisynthetic macrolide antibiotic derived from erythromycin, inhibits bacterial protein synthesis by binding to the bacterial 50S ribosomal subunit. Binding inhibits peptidyl transferase activity and interferes with amino acid translocation during the translation and protein assembly process. Clarithromycin may be bacteriostatic or bactericidal depending on the organism and drug concentration.
Structure
Thumb
Synonyms
ValueSource
6-O-MethylerythromycinChEBI
6-O-Methylerythromycin aChEBI
CLAChEBI
ClarithromycinaChEBI
ClarithromycineChEBI
ClarithromycinumChEBI
ClathromycinHMDB
BiaxinMeSH
Chemical FormulaC38H69NO13
Average Molecular Weight747.9534
Monoisotopic Molecular Weight747.476891299
IUPAC Name(3R,4S,5S,6R,7R,9R,11R,12R,13S,14R)-6-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-14-ethyl-12,13-dihydroxy-4-{[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy}-7-methoxy-3,5,7,9,11,13-hexamethyl-1-oxacyclotetradecane-2,10-dione
Traditional Nameclarithromycin
CAS Registry Number81103-11-9
SMILES
[H][C@@]1(C[C@@](C)(OC)[C@@H](O)[C@H](C)O1)O[C@H]1[C@H](C)[C@@H](O[C@]2([H])O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@@](C)(C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@](C)(O)[C@@H](CC)OC(=O)[C@@H]1C)OC
InChI Identifier
InChI=1S/C38H69NO13/c1-15-26-38(10,45)31(42)21(4)28(40)19(2)17-37(9,47-14)33(52-35-29(41)25(39(11)12)16-20(3)48-35)22(5)30(23(6)34(44)50-26)51-27-18-36(8,46-13)32(43)24(7)49-27/h19-27,29-33,35,41-43,45H,15-18H2,1-14H3/t19-,20-,21+,22+,23-,24+,25+,26-,27+,29-,30+,31-,32+,33-,35+,36-,37-,38-/m1/s1
InChI KeyAGOYDEPGAOXOCK-KCBOHYOISA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganooxygen compounds
Direct ParentAminoglycosides
Alternative Parents
Substituents
  • Aminoglycoside core
  • Macrolide
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Monosaccharide
  • Tertiary alcohol
  • 1,2-aminoalcohol
  • Amino acid or derivatives
  • Carboxylic acid ester
  • Ketone
  • Cyclic ketone
  • Tertiary aliphatic amine
  • Tertiary amine
  • Secondary alcohol
  • Lactone
  • Acetal
  • Carboxylic acid derivative
  • Dialkyl ether
  • Ether
  • Oxacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Alcohol
  • Amine
  • Organopnictogen compound
  • Organonitrogen compound
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition
Biological Location:
Subcellular:
Biofluid and excreta:
Role
Industrial application:
Pharmaceutical industry:
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point217 - 220 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility2.17e-01 g/LNot Available
LogP1.7Not Available
Predicted Properties
PropertyValueSource
Water Solubility0.22 mg/mLALOGPS
logP3.18ALOGPS
logP3.24ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)12.46ChemAxon
pKa (Strongest Basic)8.38ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area182.91 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity190.79 m3·mol-1ChemAxon
Polarizability82.03 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , PositiveNot Available
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-3900020000-7d6e24fdb4aaa06a54bdView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0005-0300060900-61dad109d1b621f69b3bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0900020000-0595f7fefa3c09c779d2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0900000000-8a6bb2526f5f15604524View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0900000000-5d02e103d637084e4b49View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0002-0000000900-9b3927ca525e74f19cecView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-052e-0800070900-da3f6b9dcca7ec506f23View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-00di-0000001900-bcb836ce99019295a00eView in MoNA
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
  • Membrane
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
Clarithromycin PathwayPw000346Pw000346 greyscalePw000346 simpleNot Available
Displaying 1 entry
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB01211 details
UrineExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB01211 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01211
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10342604
KEGG Compound IDC06912
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkClarithromycin
NuGOwiki LinkHMDB0015342
METLIN IDNot Available
PubChem Compound84029
PDB IDCTY
ChEBI ID3732
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Authors unspecified: Clarithromycin. Tuberculosis (Edinb). 2008 Mar;88(2):92-5. doi: 10.1016/S1472-9792(08)70005-2. [PubMed:18486039 ]
  2. Zuckerman JM, Qamar F, Bono BR: Macrolides, ketolides, and glycylcyclines: azithromycin, clarithromycin, telithromycin, tigecycline. Infect Dis Clin North Am. 2009 Dec;23(4):997-1026, ix-x. doi: 10.1016/j.idc.2009.06.013. [PubMed:19909895 ]
  3. Piscitelli SC, Danziger LH, Rodvold KA: Clarithromycin and azithromycin: new macrolide antibiotics. Clin Pharm. 1992 Feb;11(2):137-52. [PubMed:1312921 ]
  4. Peters DH, Clissold SP: Clarithromycin. A review of its antimicrobial activity, pharmacokinetic properties and therapeutic potential. Drugs. 1992 Jul;44(1):117-64. [PubMed:1379907 ]
  5. Stephenson GA, Stowell JG, Toma PH, Pfeiffer RR, Byrn SR: Solid-state investigations of erythromycin A dihydrate: structure, NMR spectroscopy, and hygroscopicity. J Pharm Sci. 1997 Nov;86(11):1239-44. [PubMed:9383733 ]
  6. Malhotra-Kumar S, Lammens C, Coenen S, Van Herck K, Goossens H: Effect of azithromycin and clarithromycin therapy on pharyngeal carriage of macrolide-resistant streptococci in healthy volunteers: a randomised, double-blind, placebo-controlled study. Lancet. 2007 Feb 10;369(9560):482-90. [PubMed:17292768 ]

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. Zuckerman JM, Qamar F, Bono BR: Macrolides, ketolides, and glycylcyclines: azithromycin, clarithromycin, telithromycin, tigecycline. Infect Dis Clin North Am. 2009 Dec;23(4):997-1026, ix-x. doi: 10.1016/j.idc.2009.06.013. [PubMed:19909895 ]
  2. Authors unspecified: Clarithromycin. Tuberculosis (Edinb). 2008 Mar;88(2):92-5. doi: 10.1016/S1472-9792(08)70005-2. [PubMed:18486039 ]
  3. 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 ]
  4. Williams JA, Ring BJ, Cantrell VE, Jones DR, Eckstein J, Ruterbories K, Hamman MA, Hall SD, Wrighton SA: Comparative metabolic capabilities of CYP3A4, CYP3A5, and CYP3A7. Drug Metab Dispos. 2002 Aug;30(8):883-91. [PubMed:12124305 ]
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:
CYP2C19
Uniprot ID:
P33261
Molecular weight:
55944.565
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 ]
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 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:
CYP3A5
Uniprot ID:
P20815
Molecular weight:
57108.065
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 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:
CYP3A7
Uniprot ID:
P24462
Molecular weight:
57525.03
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 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:
CYP1A2
Uniprot ID:
P05177
Molecular weight:
58406.915
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 ]

Transporters

General function:
Involved in ATP binding
Specific function:
Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells
Gene Name:
ABCB1
Uniprot ID:
P08183
Molecular weight:
141477.3
References
  1. Polli JW, Wring SA, Humphreys JE, Huang L, Morgan JB, Webster LO, Serabjit-Singh CS: Rational use of in vitro P-glycoprotein assays in drug discovery. J Pharmacol Exp Ther. 2001 Nov;299(2):620-8. [PubMed:11602674 ]
  2. Wang EJ, Casciano CN, Clement RP, Johnson WW: Active transport of fluorescent P-glycoprotein substrates: evaluation as markers and interaction with inhibitors. Biochem Biophys Res Commun. 2001 Nov 30;289(2):580-5. [PubMed:11716514 ]
  3. Egashira K, Ohtani H, Itoh S, Koyabu N, Tsujimoto M, Murakami H, Sawada Y: Inhibitory effects of pomelo on the metabolism of tacrolimus and the activities of CYP3A4 and P-glycoprotein. Drug Metab Dispos. 2004 Aug;32(8):828-33. [PubMed:15258108 ]
  4. Authors unspecified: Clarithromycin. Tuberculosis (Edinb). 2008 Mar;88(2):92-5. doi: 10.1016/S1472-9792(08)70005-2. [PubMed:18486039 ]
  5. Dey S, Gunda S, Mitra AK: Pharmacokinetics of erythromycin in rabbit corneas after single-dose infusion: role of P-glycoprotein as a barrier to in vivo ocular drug absorption. J Pharmacol Exp Ther. 2004 Oct;311(1):246-55. Epub 2004 Jun 2. [PubMed:15175422 ]
General function:
Involved in transmembrane transport
Specific function:
Mediates sodium-independent multispecific organic anion transport. Transport of prostaglandin E2, prostaglandin F2, tetracycline, bumetanide, estrone sulfate, glutarate, dehydroepiandrosterone sulfate, allopurinol, 5-fluorouracil, paclitaxel, L-ascorbic acid, salicylate, ethotrexate, and alpha- ketoglutarate
Gene Name:
SLC22A7
Uniprot ID:
Q9Y694
Molecular weight:
60025.0
References
  1. Kobayashi Y, Sakai R, Ohshiro N, Ohbayashi M, Kohyama N, Yamamoto T: Possible involvement of organic anion transporter 2 on the interaction of theophylline with erythromycin in the human liver. Drug Metab Dispos. 2005 May;33(5):619-22. Epub 2005 Feb 11. [PubMed:15708966 ]