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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2020-02-26 21:39:57 UTC
HMDB IDHMDB0014596
Secondary Accession Numbers
  • HMDB14596
Metabolite Identification
Common NameClomocycline
DescriptionClomocycline is only found in individuals that have used or taken this drug. It is a tetracycline antibiotic.Clomocycline inhibits cell growth by inhibiting translation. It binds to the 30S ribosomal subunit and prevents the amino-acyl tRNA from binding to the A site of the ribosome. The binding is reversible in nature. Clomocycline is lipophilic and can easily pass through the cell membrane or passively diffuses through porin channels in the bacterial membrane.
Structure
Data?1582753197
Synonyms
ValueSource
ChlormethylenecyclineChEBI
ClomocyclinaChEBI
ClomocyclinumChEBI
Chemical FormulaC23H25ClN2O9
Average Molecular Weight508.906
Monoisotopic Molecular Weight508.124858115
IUPAC Name(4S,4aS,5aS,6S,12aS)-7-chloro-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-N-(hydroxymethyl)-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide
Traditional Name甲氯环素
CAS Registry Number1181-54-0
SMILES
[H][C@@]12C[C@@]3([H])C(=C(O)[C@]1(O)C(=O)C(C(=O)NCO)=C(O)[C@H]2N(C)C)C(=O)C1=C(O)C=CC(Cl)=C1[C@@]3(C)O
InChI Identifier
InChI=1S/C23H25ClN2O9/c1-22(34)8-6-9-16(26(2)3)18(30)14(21(33)25-7-27)20(32)23(9,35)19(31)12(8)17(29)13-11(28)5-4-10(24)15(13)22/h4-5,8-9,16,27-28,30-31,34-35H,6-7H2,1-3H3,(H,25,33)/t8-,9-,16-,22-,23-/m0/s1
InChI KeyGJGDLRSSCNAKGL-KMVLDZISSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetracyclines. These are polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassTetracyclines
Sub ClassNot Available
Direct ParentTetracyclines
Alternative Parents
Substituents
  • Tetracycline
  • Naphthacene
  • Tetracene
  • Anthracene carboxylic acid or derivatives
  • Tetralin
  • Aryl ketone
  • 1-hydroxy-2-unsubstituted benzenoid
  • Cyclohexenone
  • Aralkylamine
  • Aryl chloride
  • Aryl halide
  • Benzenoid
  • Vinylogous acid
  • Tertiary alcohol
  • Amino acid or derivatives
  • Carboxamide group
  • Ketone
  • Secondary carboxylic acid amide
  • Tertiary aliphatic amine
  • Tertiary amine
  • Polyol
  • Alkanolamine
  • Carboxylic acid derivative
  • Enol
  • Organic nitrogen compound
  • Amine
  • Organic oxide
  • Hydrocarbon derivative
  • Organohalogen compound
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Organochloride
  • Alcohol
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility1.77 g/LNot Available
LogP0.2Not Available
Predicted Properties
PropertyValueSource
Water Solubility1.77 g/LALOGPS
logP-0.45ALOGPS
logP-3.3ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)0.013ChemAxon
pKa (Strongest Basic)8.23ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area187.86 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity124.99 m³·mol⁻¹ChemAxon
Polarizability49.29 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0btc-4259500000-52acd2cb0d6edb49efb3Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-000i-4340249000-8efc7ea409a53d2bac64Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-054o-0000920000-2346ee966df9629081eaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-1000900000-3ccd2788dd663e4263efSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0292-3006900000-490e3bac510d38e0d722Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-2100940000-df0b3ace5f26ce112a6fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a7l-3000900000-dc998119e27d1771ba49Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9007200000-a3926451080077e96257Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00453 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00453 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00453
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID21251443
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkClomocycline
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID59589
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available