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Record Information
Version3.6
Creation Date2012-09-06 15:16:49 UTC
Update Date2016-02-11 01:28:25 UTC
HMDB IDHMDB14401
Secondary Accession NumbersNone
Metabolite Identification
Common NameLymecycline
DescriptionLymecycline is only found in individuals that have used or taken this drug. It is a tetracycline with a 7-chloro substitution.Lymecycline 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. Lymecycline is lipophilic and can easily pass through the cell membrane or passively diffuses through porin channels in the bacterial membrane. Cells become resistant to lymecycline by at least two mechanisms: efflux and ribosomal protection. In efflux, a resistance gene encodes a membrane protein that actively pumps lymecycline 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 lymecycline from acting on the ribosome.
Structure
Thumb
Synonyms
ValueSource
(+)-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-carboxamideChEBI
LimeciclinaChEBI
LymecyclinumChEBI
N-LysinomethyltetracyclineChEBI
N(2)-(((+)-5-amino-5-carboxypentylamino)Methyl)tetracyclineChEBI
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)lysineChEBI
Tetracycline-L-methylene lysineChEBI
Tetracycline-L-methylenelysineChEBI
7-ChlorotetracyclineHMDB
ChlorotetracyclineHMDB
ChlortetracyclinHMDB
ChlortetracyclineHMDB
Chlortetracyclinium chlorideHMDB
CLTCHMDB
Chemical FormulaC29H38N4O10
Average Molecular Weight602.6328
Monoisotopic Molecular Weight602.258793456
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
CAS Registry Number992-21-2
SMILES
[H][C@@]12C[C@@]3([H])C(C(=O)C4=C(O)C=CC=C4[C@@]3(C)O)=C(O)[C@]1(O)C(=O)C(C(=O)NCNCCCC[C@H](N)C(O)=O)=C(O)[C@H]2N(C)C
InChI Identifier
InChI=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
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
  • L-alpha-amino acid
  • Tetralin
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Carbocyclic fatty acid
  • Aryl ketone
  • Medium-chain fatty acid
  • Aralkylamine
  • Amino fatty acid
  • Fatty acyl
  • Benzenoid
  • Vinylogous acid
  • Tertiary alcohol
  • Tertiary aliphatic amine
  • Tertiary amine
  • Secondary carboxylic acid amide
  • Polyol
  • Ketone
  • Carboxamide group
  • Secondary amine
  • Monocarboxylic acid or derivatives
  • Enol
  • Secondary aliphatic amine
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Drug
Biofunction
  • Anti-Bacterial Agents
  • Antiprotozoal Agents
  • Antiprotozoals
  • Protein Synthesis Inhibitors
  • Tetracyclines
Application
  • Pharmaceutical
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility1.31e+00 g/LNot Available
LogP0.3Not Available
Predicted Properties
PropertyValueSource
Water Solubility1.31 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count10ChemAxon
Refractivity154.51 m3·mol-1ChemAxon
Polarizability62.88 Å3ChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Lymecycline PathwaySMP00295Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00256
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00256
  • Not Applicable
details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiofluidValueOriginal ageOriginal sexOriginal conditionComments
Blood0-2 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0-1 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00256
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID20121315
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkLymecycline
NuGOwiki LinkHMDB14401
Metagene LinkHMDB14401
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID59040
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Meynadier J, Alirezai M: Systemic antibiotics for acne. Dermatology. 1998;196(1):135-9. [9557248 ]
  2. MEDSAFE [Link]