Lymecycline (T3D3952)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (1)XML
Targets (1)
Record Information
Version2.0
Creation Date2014-08-28 19:48:07 UTC
Update Date2014-12-24 20:26:34 UTC
Accession NumberT3D3952
Identification
Common NameLymecycline
ClassSmall Molecule
DescriptionLymecycline is a tetracycline broad-spectrum antibiotic marketed by the pharmaceutical company Galderma. It is approximately 5,000 times more soluble than tetracycline base and is unique amongst tetracyclines in that it is absorbed by an active transport process across the intestinal wall, making use of the same fast and efficient mechanism by which carbohydrates are absorbed.
Compound Type
  • Anti-Bacterial Agent
  • Antiprotozoal Agent
  • Drug
  • Metabolite
  • Organic Compound
  • Synthetic Compound
  • Tetracycline
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
(+)-N-(5-Amino-5-carboxypentylaminomethyl)-4-dimethylamino-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxonaphthacene-2-carboxamide
7-Chlorotetracycline
Chlorotetracycline
Chlortetracyclin
Chlortetracycline
Chlortetracyclinium chloride
CLTC
Eficiclina
Limeciclina
Lymecyclinum
N(2)-(((+)-5-Amino-5-carboxypentylamino)methyl)tetracycline
N-Lysinomethyltetracycline
N6-((4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamido)methyl)lysine
Tetracycline-L-methylene lysine
Tetracycline-L-methylenelysine
Tetralisal
Tetralysal
Chemical FormulaC29H38N4O10
Average Molecular Mass602.633 g/mol
Monoisotopic Mass602.259 g/mol
CAS Registry Number992-21-2
IUPAC Name(2S)-6-[({[(4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracen-2-yl]formamido}methyl)amino]-2-aminohexanoic acid
Traditional Namelymecycline
SMILES[H][C@](N)(CCCCNCN=C(O)C1=C(O)[C@@]([H])(N(C)C)[C@]2([H])C[C@@]3([H])C(C(=O)C4=C(C=CC=C4O)[C@@]3(C)O)=C(O)[C@]2(O)C1=O)C(O)=O
InChI IdentifierInChI=1S/C29H38N4O10/c1-28(42)13-7-6-9-17(34)18(13)22(35)19-14(28)11-15-21(33(2)3)23(36)20(25(38)29(15,43)24(19)37)26(39)32-12-31-10-5-4-8-16(30)27(40)41/h6-7,9,14-16,21,31,34,36-37,42-43H,4-5,8,10-12,30H2,1-3H3,(H,32,39)(H,40,41)/t14-,15-,16-,21-,28+,29-/m0/s1
InChI KeyInChIKey=AHEVKYYGXVEWNO-UEPZRUIBSA-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
  • L-alpha-amino acid
  • Alpha-amino acid
  • Alpha-amino acid or derivatives
  • Aryl ketone
  • Medium-chain fatty acid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Amino fatty acid
  • Cyclohexenone
  • 1-hydroxy-4-unsubstituted benzenoid
  • Aralkylamine
  • Hydroxy fatty acid
  • Fatty acyl
  • Benzenoid
  • Vinylogous acid
  • Tertiary alcohol
  • Amino acid
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Amino acid or derivatives
  • Ketone
  • Tertiary amine
  • Tertiary aliphatic amine
  • Secondary amine
  • Carboxylic acid derivative
  • Carboxylic acid
  • Secondary aliphatic amine
  • Enol
  • Polyol
  • Monocarboxylic acid or derivatives
  • Amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Carbonyl group
  • Organopnictogen compound
  • Primary amine
  • Organic oxide
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Cytoplasm
  • Membrane
Biofluid LocationsNot Available
Tissue Locations
  • Bone Marrow
  • Heart
  • Liver
Pathways
NameSMPDB LinkKEGG Link
Lymecycline Action PathwaySMP00295 Not Available
Applications
Biological Roles
Chemical Roles
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilitySoluble (at all physiological pH values)
LogP0.3
Predicted Properties
PropertyValueSource
Water Solubility1.31 g/LALOGPS
logP-0.27ALOGPS
logP-8.3ChemAxon
logS-2.7ALOGPS
pKa (Strongest Acidic)0.4ChemAxon
pKa (Strongest Basic)9.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area242.98 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity154.51 m³·mol⁻¹ChemAxon
Polarizability62.88 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a5i-3019250000-12eac72ab7dedd803b342017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0a4i-5005649000-3f203b4cc7bb2470c6492017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0200091000-89e41c2e3834190df2012016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001r-6700590000-4e361cb29ebc1a76bb632016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-9828330000-d0ae1ca5167e192c6d342016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0322669000-c5830c776faedf57e4382016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0f89-1735931000-4014754799d6e18776552016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0ntd-5549300000-866a3d185c36d9e549e22016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f89-1410098000-d903d835ba62ec246e532021-09-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-8439164000-3f302bf25f25bb5e551a2021-09-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9101230000-d4f12ffa94a44190d8e82021-09-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0100291000-3fa58d959484de3466ac2021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-015i-2100791000-ba5e16a41c66bdd2f8ae2021-09-24View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-9310100000-419827f97c772d16a6942021-09-24View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-25View Spectrum
Toxicity Profile
Route of ExposureAbsorption is fast and efficient. Bioavailability is 100% following oral administration.
Mechanism of ToxicityTetracyclines target the 28S small subunit of the mitochondrial ribosome thereby deactivation mitochondrial protein synthesis. As a result tetracyclines are cytotoxic to the most metabolically active cells or tissues including the heart, liver, thymus and bone-marrow. (2). The likely target of most tetracyclines is the 12S rRNA molecule in the mitochondrial ribosome, which is analogous to the 16S rRNA in bacterial ribosomes.
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesFor the treatment of 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. Lymecycline 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.
Minimum Risk LevelNot Available
Health EffectsSide effects from normal doses of tetracyclines are relatively minimal, but of particular note is phototoxicity. Tetracylclines increase the risk of sunburn under exposure to light from the sun or other sources. Tetracyclines may also cause stomach or bowel upsets, and, on rare occasions, allergic reactions. Very rarely, severe headache and vision problems may be signs of dangerous secondary intracranial hypertension, also known as pseudotumor cerebri. Tetracyclines are teratogens and cause tooth discolouration and poor tooth mineralization in the fetus as they develop in infancy. Symptoms of tetracycline overdose include anorexia, nausea, diarrhea, glossitis, dysphagia, enterocolitis and inflammatory lesions, skin reactions such as maculopapular and erythematous rashes, exfoliative dermatitis, photosensitivity, hypersensitivity reactions such as urticaria, angioneurotic oedema, anaphylaxis, anaphyl-actoid purpura, pericarditis, and exacerbation of systemic lupus erythematosus, benign intracranial hypertension in adults disappearing on discontinuation of the medicine, haematologic abnormalities such as haemolytic anaemia, thrombocytopenia, neutropenia, and eosinophilia.
SymptomsSymptoms include nausea, vomiting, diarrhoea, glossitis, enterocolitis, dysphagia, dermatitis, hypersensitivity reactions, proctitis, and vaginitis.
TreatmentDrug therapy is discontinued immediately; exchange transfusion may be required to remove the drug. Sometimes, phenobarbital (UGT induction) is used.
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB00256
HMDB IDHMDB14401
PubChem Compound ID24757945
ChEMBL IDCHEMBL2103929
ChemSpider ID23501197
KEGG IDNot Available
UniProt IDNot Available
OMIM ID
ChEBI ID59040
BioCyc IDNot Available
CTD IDNot Available
Stitch IDNot Available
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkLymecycline
References
Synthesis Reference

Willis L. Winstrom, “Process and apparatus for the preparation of chlortetracycline-containing animal feed compositions.” U.S. Patent US06844006, issued January 18, 2005.

MSDST3D3952.pdf
General References
  1. Meynadier J, Alirezai M: Systemic antibiotics for acne. Dermatology. 1998;196(1):135-9. [9557248 ]
  2. McKee EE, Ferguson M, Bentley AT, Marks TA: Inhibition of mammalian mitochondrial protein synthesis by oxazolidinones. Antimicrob Agents Chemother. 2006 Jun;50(6):2042-9. [16723564 ]
  3. Wikipedia. Lymecycline. Last updated on 31 March 2014. [Link]
  4. Link [Link]
  5. MEDSAFE [Link]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

Target Details
1. 12S RNA
Binding/Activity Constants
TypeValueAssay TypeAssay Source
Inhibitory2.00 uMNot AvailableNot Available