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Identification
NameClomocycline
Accession NumberDB00453  (APRD00343)
TypeSmall Molecule
GroupsApproved
DescriptionClomocycline is a tetracycline antibiotic.
Structure
Thumb
Synonyms
Chlormethylenecycline
Clomociclina
Clomocyclina
Clomocyclinum
External Identifiers Not Available
Approved Prescription ProductsNot Available
Approved Generic Prescription ProductsNot Available
Approved Over the Counter ProductsNot Available
Unapproved/Other Products Not Available
International BrandsNot Available
Brand mixturesNot Available
SaltsNot Available
Categories
UNIIYP0241BU76
CAS number1181-54-0
WeightAverage: 508.906
Monoisotopic: 508.124858115
Chemical FormulaC23H25ClN2O9
InChI KeyGJGDLRSSCNAKGL-KMVLDZISSA-N
InChI
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
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
SMILES
[H][C@@]12C[C@@]3([H])C(=C(O)[C@]1(O)C(=O)C(C(=O)NCO)=C(O)[[email protected]]2N(C)C)C(=O)C1=C(O)C=CC(Cl)=C1[C@@]3(C)O
Pharmacology
IndicationFor the treatment and management of Brucellosis, mycoplasma infection, acne vulgaris, chlamydial infection;Chronic bronchitis
Structured Indications Not Available
PharmacodynamicsClomocycline is a tetracycline antibiotic that is commonly prescribed by medical doctors for infections and to treat acne. It may also be used to treat urinary tract infections, gum disease, and other bacterial infections such as gonorrhea and chlamydia. Clomocycline is also used commonly as a prophylactic treatment for infection by Bacillus anthracis (anthrax). It is also effective against Yersinia pestis and malaria and is also prescribed for the treatment of Lyme disease. 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. Cells become resistant to Clomocycline by at least two mechanisms: efflux and ribosomal protection. In efflux, a resistance gene encodes a membrane protein that actively pumps Clomocycline out of the cell. This is the mechanism of action of the tetracycline resistance gene on the artificial plasmid pBR322. In ribosomal protection, a resistance gene encodes a protein which binds to the ribosome and prevents Clomocycline from acting on the ribosome.
Mechanism of actionClomocycline 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.
TargetKindPharmacological actionActionsOrganismUniProt ID
30S ribosomal protein S4Proteinyes
inhibitor
Escherichia coli (strain K12)P0A7V8 details
30S ribosomal protein S9Proteinunknown
inhibitor
Escherichia coli (strain K12)P0A7X3 details
16S rRNANucleotideno
inhibitor
Enteric bacteria and other eubacterianot applicabledetails
Related Articles
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
MetabolismNot Available
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organisms
  • Enteric bacteria and other eubacteria
Pathways
PathwayCategorySMPDB ID
Clomocycline Action PathwayDrug actionSMP00262
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available
References
Synthesis ReferenceNot Available
General ReferencesNot Available
External Links
ATC CodesJ01AA11
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
ADMET
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.6317
Blood Brain Barrier-0.9659
Caco-2 permeable-0.5295
P-glycoprotein substrateSubstrate0.8364
P-glycoprotein inhibitor INon-inhibitor0.846
P-glycoprotein inhibitor IIInhibitor0.551
Renal organic cation transporterNon-inhibitor0.8954
CYP450 2C9 substrateNon-substrate0.7461
CYP450 2D6 substrateNon-substrate0.8278
CYP450 3A4 substrateSubstrate0.6882
CYP450 1A2 substrateNon-inhibitor0.8305
CYP450 2C9 inhibitorNon-inhibitor0.8343
CYP450 2D6 inhibitorNon-inhibitor0.8658
CYP450 2C19 inhibitorNon-inhibitor0.8104
CYP450 3A4 inhibitorNon-inhibitor0.8207
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.5532
Ames testNon AMES toxic0.7312
CarcinogenicityNon-carcinogens0.8924
BiodegradationNot ready biodegradable0.9951
Rat acute toxicity2.4234 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9898
hERG inhibition (predictor II)Inhibitor0.5484
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397 )
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental Properties
PropertyValueSource
logP0.2Not Available
Predicted Properties
PropertyValueSource
Water Solubility1.77 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count3ChemAxon
Refractivity124.99 m3·mol-1ChemAxon
Polarizability49.29 Å3ChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
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
Taxonomy
DescriptionThis compound 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
  • Tetracene
  • Naphthacene
  • Anthracene carboxylic acid or derivatives
  • Tetralin
  • Aryl ketone
  • 4-halophenol
  • Aralkylamine
  • Aryl halide
  • Aryl chloride
  • Vinylogous acid
  • Tertiary alcohol
  • Tertiary aliphatic amine
  • Tertiary amine
  • Secondary carboxylic acid amide
  • Polyol
  • Ketone
  • Carboxamide group
  • Enol
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Alkanolamine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors

Targets

Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
yes
Actions
inhibitor
General Function:
Translation repressor activity, nucleic acid binding
Specific Function:
One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity muta...
Gene Name:
rpsD
Uniprot ID:
P0A7V8
Molecular Weight:
23468.915 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
unknown
Actions
inhibitor
General Function:
Trna binding
Specific Function:
The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.
Gene Name:
rpsI
Uniprot ID:
P0A7X3
Molecular Weight:
14856.105 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
3. 16S rRNA
Kind
Nucleotide
Organism
Enteric bacteria and other eubacteria
Pharmacological action
no
Actions
inhibitor
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Toledo H, Lopez-Solis R: Tetracycline resistance in Chilean clinical isolates of Helicobacter pylori. J Antimicrob Chemother. 2010 Mar;65(3):470-3. doi: 10.1093/jac/dkp457. Epub 2009 Dec 24. [PubMed:20035020 ]
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Drug created on June 13, 2005 07:24 / Updated on August 17, 2016 12:23