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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-07-09 16:13:00 UTC
Update Date2021-09-14 15:44:48 UTC
HMDB IDHMDB0061020
Secondary Accession Numbers
  • HMDB61020
Metabolite Identification
Common NameN-desmethylclarithromycin
DescriptionN-desmethylclarithromycin is a metabolite of clarithromycin. Clarithromycin is a macrolide antibiotic used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), skin and skin structure infections. In addition, it is sometimes used to treat Legionellosis, Helicobacter pylori, and lyme disease. (Wikipedia)
Structure
Data?1563866135
SynonymsNot Available
Chemical FormulaC37H67NO13
Average Molecular Weight733.9268
Monoisotopic Molecular Weight733.461241235
IUPAC Name(3R,4R,6S,7S,9R,11R,12R,13S,14R)-14-ethyl-12,13-dihydroxy-4-{[(2S,4S,5R,6R)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy}-6-{[(2R,3S,4R,6S)-3-hydroxy-6-methyl-4-(methylamino)oxan-2-yl]oxy}-7-methoxy-3,5,7,9,11,13-hexamethyl-1-oxacyclotetradecane-2,10-dione
Traditional Name(3R,4R,6S,7S,9R,11R,12R,13S,14R)-14-ethyl-12,13-dihydroxy-4-{[(2S,4S,5R,6R)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy}-6-{[(2R,3S,4R,6S)-3-hydroxy-6-methyl-4-(methylamino)oxan-2-yl]oxy}-7-methoxy-3,5,7,9,11,13-hexamethyl-1-oxacyclotetradecane-2,10-dione
CAS Registry NumberNot Available
SMILES
CC[C@H]1OC(=O)[C@H](C)[C@H](O[C@@H]2C[C@](C)(OC)[C@H](O)[C@@H](C)O2)C(C)[C@H](O[C@H]2O[C@@H](C)C[C@@H](NC)[C@@H]2O)[C@](C)(C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O)OC
InChI Identifier
InChI=1S/C37H67NO13/c1-14-25-37(10,44)30(41)20(4)27(39)18(2)16-36(9,46-13)32(51-34-28(40)24(38-11)15-19(3)47-34)21(5)29(22(6)33(43)49-25)50-26-17-35(8,45-12)31(42)23(7)48-26/h18-26,28-32,34,38,40-42,44H,14-17H2,1-13H3/t18-,19+,20+,21?,22-,23-,24-,25-,26-,28+,29-,30-,31-,32+,34-,35+,36+,37-/m1/s1
InChI KeyCIJTVUQEURKBDL-ZVGWNXEOSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentAminoglycosides
Alternative Parents
Substituents
  • Aminoglycoside core
  • Macrolide
  • Glycosyl compound
  • O-glycosyl compound
  • Monosaccharide
  • Oxane
  • Tertiary alcohol
  • 1,2-aminoalcohol
  • Secondary alcohol
  • Cyclic ketone
  • Amino acid or derivatives
  • Lactone
  • Ketone
  • Carboxylic acid ester
  • Secondary amine
  • Organoheterocyclic compound
  • Oxacycle
  • Acetal
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Ether
  • Secondary aliphatic amine
  • Dialkyl ether
  • Organonitrogen compound
  • Organopnictogen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Organic oxide
  • Amine
  • Alcohol
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.19 g/LALOGPS
logP2.67ALOGPS
logP2.86ChemAxon
logS-3.6ALOGPS
pKa (Strongest Acidic)12.46ChemAxon
pKa (Strongest Basic)9.54ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area191.7 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity185.49 m³·mol⁻¹ChemAxon
Polarizability78.75 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+247.79130932474
DeepCCS[M-H]-246.06730932474
DeepCCS[M-2H]-280.130932474
DeepCCS[M+Na]+254.00230932474
AllCCS[M+H]+260.332859911
AllCCS[M+H-H2O]+259.832859911
AllCCS[M+NH4]+260.832859911
AllCCS[M+Na]+260.932859911
AllCCS[M-H]-258.332859911
AllCCS[M+Na-2H]-263.832859911
AllCCS[M+HCOO]-270.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-desmethylclarithromycinCC[C@H]1OC(=O)[C@H](C)[C@H](O[C@@H]2C[C@](C)(OC)[C@H](O)[C@@H](C)O2)C(C)[C@H](O[C@H]2O[C@@H](C)C[C@@H](NC)[C@@H]2O)[C@](C)(C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O)OC3341.4Standard polar33892256
N-desmethylclarithromycinCC[C@H]1OC(=O)[C@H](C)[C@H](O[C@@H]2C[C@](C)(OC)[C@H](O)[C@@H](C)O2)C(C)[C@H](O[C@H]2O[C@@H](C)C[C@@H](NC)[C@@H]2O)[C@](C)(C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O)OC4354.0Standard non polar33892256
N-desmethylclarithromycinCC[C@H]1OC(=O)[C@H](C)[C@H](O[C@@H]2C[C@](C)(OC)[C@H](O)[C@@H](C)O2)C(C)[C@H](O[C@H]2O[C@@H](C)C[C@@H](NC)[C@@H]2O)[C@](C)(C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@]1(C)O)OC4432.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (Non-derivatized) - 70eV, Positivesplash10-00kf-9400011500-abfe25bbc9b035797f9f2017-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_1_7) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_12) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_13) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_14) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_15) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_16) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-desmethylclarithromycin GC-MS (TMS_2_17) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 10V, Positive-QTOFsplash10-05u6-0100190400-e18a88a37c8214ba13792017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 20V, Positive-QTOFsplash10-053r-0300980000-31acdad1d1ace3203cd22017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 40V, Positive-QTOFsplash10-00lr-8200960000-f803ae06d804681c797e2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 10V, Negative-QTOFsplash10-01qi-0500080900-c9fc4a49c0747438ada82017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 20V, Negative-QTOFsplash10-022i-0200290200-a7945b485a28dd9f215f2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 40V, Negative-QTOFsplash10-0ab9-9300840000-9ae7e0743f2f38f26d452017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 10V, Positive-QTOFsplash10-001i-0000010900-ffaf8909547541d6dccf2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 20V, Positive-QTOFsplash10-004i-1900072400-197c3a8004ab1bfc0dc42021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 40V, Positive-QTOFsplash10-057l-9700000000-f844e4688ca8d4a312092021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 10V, Negative-QTOFsplash10-001i-0000000900-c24ed69e93bbfed40bb12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 20V, Negative-QTOFsplash10-01q9-0900000500-f0a00cdf361b35b59bad2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-desmethylclarithromycin 40V, Negative-QTOFsplash10-004l-4900010300-3956c1bdf1e818ae9aca2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131770004
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available