ContaminantDB: Lymecycline

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Targets (2)XML

Record Information

Version

1.0

Creation Date

2014-08-28 19:48:07 UTC

Update Date

2026-05-14 16:24:58 UTC

Accession Number

CHEM002912

Identification

Common Name

Lymecycline

Class

Small Molecule

Description

Lymecycline 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.

Contaminant Sources

HMDB Contaminants - Urine
T3DB toxins
ToxCast & Tox21 Chemicals

Contaminant Type

Anti-Bacterial Agent
Antiprotozoal Agent
Drug
Metabolite
Organic Compound
Synthetic Compound
Tetracycline

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(+)-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	ChEBI
Limeciclina	ChEBI
Lymecyclinum	ChEBI
N-Lysinomethyltetracycline	ChEBI
N(2)-(((+)-5-Amino-5-carboxypentylamino)methyl)tetracycline	ChEBI
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	ChEBI
Tetracycline-L-methylene lysine	ChEBI
Tetracycline-L-methylenelysine	ChEBI
7-Chlorotetracycline	HMDB
Chlorotetracycline	HMDB
Chlortetracyclin	HMDB
Chlortetracycline	HMDB
Chlortetracyclinium chloride	HMDB
CLTC	HMDB

Chemical Formula

C₂₉H₃₈N₄O₁₀

Average Molecular Mass

602.633 g/mol

Monoisotopic Mass

602.259 g/mol

CAS Registry Number

992-21-2

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 Name

lymecycline

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 Key

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.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tetracyclines

Sub Class

Not Available

Direct Parent

Tetracyclines

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 Framework

Aromatic homopolycyclic compounds

External Descriptors

tetracyclines (CHEBI:59040 )

Biological Properties

Status

Detected and Not Quantified

Origin

Exogenous

Cellular Locations

Cytoplasm
Membrane

Biofluid Locations

Not Available

Tissue Locations

Bone Marrow
Heart
Liver

Pathways

Name	SMPDB Link	KEGG Link
Lymecycline Action Pathway	SMP00295	Not Available

Applications

Biological Roles

Chemical Roles

protein synthesis inhibitor

Physical Properties

State

Solid

Appearance

White powder.

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Soluble (at all physiological pH values)

Predicted Properties

Property	Value	Source
Water Solubility	1.31 g/L	ALOGPS
logP	-0.27	ALOGPS
logP	-8.3	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	0.4	ChemAxon
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	242.98 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	154.51 m³·mol⁻¹	ChemAxon
Polarizability	62.88 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a5i-3019250000-12eac72ab7dedd803b34	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0a4i-5005649000-3f203b4cc7bb2470c649	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0200091000-89e41c2e3834190df201	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001r-6700590000-4e361cb29ebc1a76bb63	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9828330000-d0ae1ca5167e192c6d34	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0322669000-c5830c776faedf57e438	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0f89-1735931000-4014754799d6e1877655	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ntd-5549300000-866a3d185c36d9e549e2	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f89-1410098000-d903d835ba62ec246e53	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-8439164000-3f302bf25f25bb5e551a	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9101230000-d4f12ffa94a44190d8e8	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0100291000-3fa58d959484de3466ac	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-015i-2100791000-ba5e16a41c66bdd2f8ae	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9310100000-419827f97c772d16a694	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum

Toxicity Profile

Route of Exposure

Absorption is fast and efficient. Bioavailability is 100% following oral administration.

Mechanism of Toxicity

Tetracyclines 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.

Metabolism

Not Available

Toxicity Values

Not Available

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

For 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 Level

Not Available

Health Effects

Side 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.

Symptoms

Symptoms include nausea, vomiting, diarrhoea, glossitis, enterocolitis, dysphagia, dermatitis, hypersensitivity reactions, proctitis, and vaginitis.

Treatment

Drug therapy is discontinued immediately; exchange transfusion may be required to remove the drug. Sometimes, phenobarbital (UGT induction) is used.

Concentrations

Not Available

External Links

DrugBank ID

DB00256

HMDB ID

HMDB0014401

FooDB ID

Not Available

Phenol Explorer ID

Not Available

KNApSAcK ID

Not Available

BiGG ID

Not Available

BioCyc ID

Not Available

METLIN ID

Not Available

PDB ID

Not Available

Wikipedia Link

Lymecycline

Chemspider ID

20121315

ChEBI ID

59040

PubChem Compound ID

Not Available

Kegg Compound ID

Not Available

YMDB ID

Not Available

ECMDB ID

Not Available

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.

MSDS

Not Available

General References

1. https://www.ncbi.nlm.nih.gov/pubmed/?term=1650428

2. https://www.ncbi.nlm.nih.gov/pubmed/?term=24985054

3. https://www.ncbi.nlm.nih.gov/pubmed/?term=25672310

4. Meynadier J, Alirezai M: Systemic antibiotics for acne. Dermatology. 1998;196(1):135-9.

5. MEDSAFE: http://www.medsafe.govt.nz/profs/Datasheet/t/Tetralysalcap.pdf

Lymecycline (CHEM002912)

Structure for CHEM002912: Lymecycline