Explore a selection of our essential drug information below, or:
Identification
- Generic Name
- Clorobiocin
- DrugBank Accession Number
- DB03966
- Background
Clorobiocin is an aminocoumarin antibiotic, similar to novobiocin and coumermycin A1.
- Type
- Small Molecule
- Groups
- Experimental
- Structure
Structure for Clorobiocin (DB03966)
- Weight
- Average: 697.128
Monoisotopic: 696.208587743 - Chemical Formula
- C35H37ClN2O11
- Synonyms
- Chlorobiocin
- External IDs
- 18 631 R.P.
- 18631 RP
- Antibiotic RP 18,631
- RP 18631
Pharmacology
- Indication
Not Available
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Prevent Adverse Drug Events TodayTap into our Clinical API for life-saving information on contraindications & blackbox warnings, population restrictions, harmful risks, & more.Avoid life-threatening adverse drug events with our Clinical API- Pharmacodynamics
Not Available
- Mechanism of action
Target Actions Organism ADNA topoisomerase 2-beta inhibitorHumans ADNA topoisomerase 2-alpha inhibitorHumans UDNA gyrase subunit B Not Available Escherichia coli (strain K12) - Absorption
Not Available
- Volume of distribution
Not Available
- Protein binding
Not Available
- Metabolism
- Not Available
- Route of elimination
Not Available
- Half-life
Not Available
- Clearance
Not Available
- Adverse Effects
Improve decision support & research outcomesWith structured adverse effects data, including: blackbox warnings, adverse reactions, warning & precautions, & incidence rates. View sample adverse effects data in our new Data Library!Improve decision support & research outcomes with our structured adverse effects data.- Toxicity
Not Available
- Pathways
- Not Available
- Pharmacogenomic Effects/ADRs
- Not Available
Interactions
- Drug Interactions
- This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Drug Interaction Integrate drug-drug
interactions in your softwareAcetohexamide The therapeutic efficacy of Acetohexamide can be increased when used in combination with Clorobiocin. Chlorpropamide The therapeutic efficacy of Chlorpropamide can be increased when used in combination with Clorobiocin. Dexmethylphenidate The serum concentration of the active metabolites of Clorobiocin can be increased when Clorobiocin is used in combination with Dexmethylphenidate. Diazoxide The serum concentration of Clorobiocin can be increased when it is combined with Diazoxide. Doxycycline The therapeutic efficacy of Clorobiocin can be increased when used in combination with Doxycycline. - Food Interactions
- Not Available
Categories
- Drug Categories
- Chemical TaxonomyProvided by Classyfire
- Description
- This compound belongs to the class of organic compounds known as coumarin glycosides. These are aromatic compounds containing a carbohydrate moiety glycosidically bound to a coumarin moiety.
- Kingdom
- Organic compounds
- Super Class
- Phenylpropanoids and polyketides
- Class
- Coumarins and derivatives
- Sub Class
- Coumarin glycosides
- Direct Parent
- Coumarin glycosides
- Alternative Parents
- Phenolic glycosides / 4-hydroxycoumarins / Hexoses / O-glycosyl compounds / 1-benzopyrans / Benzamides / Pyrrole carboxylic acids and derivatives / Benzoyl derivatives / 1-hydroxy-2-unsubstituted benzenoids / Pyranones and derivatives show 19 more
- Substituents
- 1-benzopyran / 1-hydroxy-2-unsubstituted benzenoid / 4-hydroxycoumarin / Acetal / Alcohol / Aromatic heteropolycyclic compound / Aryl chloride / Aryl halide / Azacycle / Benzamide show 42 more
- Molecular Framework
- Aromatic heteropolycyclic compounds
- External Descriptors
- Not Available
- Affected organisms
- Enteric bacteria and other eubacteria
Chemical Identifiers
- UNII
- Not Available
- CAS number
- 39868-96-7
- InChI Key
- FJAQNRBDVKIIKK-LFLQOBSNSA-N
- InChI
- InChI=1S/C35H37ClN2O11/c1-16(2)7-9-18-15-19(10-13-22(18)39)31(42)38-25-26(40)20-11-14-23(24(36)28(20)47-33(25)44)46-34-27(41)29(30(45-6)35(4,5)49-34)48-32(43)21-12-8-17(3)37-21/h7-8,10-15,27,29-30,34,37,39-41H,9H2,1-6H3,(H,38,42)/t27-,29+,30-,34-/m1/s1
- IUPAC Name
- (3R,4S,5R,6S)-6-({8-chloro-4-hydroxy-3-[4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamido]-2-oxo-2H-chromen-7-yl}oxy)-5-hydroxy-3-methoxy-2,2-dimethyloxan-4-yl 5-methyl-1H-pyrrole-2-carboxylate
- SMILES
- CO[C@@H]1[C@@H](OC(=O)C2=CC=C(C)N2)[C@@H](O)[C@H](OC2=C(Cl)C3=C(C=C2)C(O)=C(NC(=O)C2=CC(CC=C(C)C)=C(O)C=C2)C(=O)O3)OC1(C)C
References
- General References
- Tsai FT, Singh OM, Skarzynski T, Wonacott AJ, Weston S, Tucker A, Pauptit RA, Breeze AL, Poyser JP, O'Brien R, Ladbury JE, Wigley DB: The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins. 1997 May;28(1):41-52. [Article]
- Cejka K, Holubova I, Hubacek J: Curing effect of clorobiocin on Escherichia coli plasmids. Mol Gen Genet. 1982;186(1):153-5. [Article]
- External Links
- KEGG Compound
- C12032
- PubChem Compound
- 54706138
- PubChem Substance
- 46505267
- ChemSpider
- 21256053
- BindingDB
- 50330317
- ChEMBL
- CHEMBL303984
- ZINC
- ZINC000004102306
- PDBe Ligand
- CBN
- Wikipedia
- Clorobiocin
- PDB Entries
- 1kzn
Clinical Trials
- Clinical Trials
Clinical Trial & Rare Diseases Add-on Data Package
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Pharmacoeconomics
- Manufacturers
- Not Available
- Packagers
- Not Available
- Dosage Forms
- Not Available
- Prices
- Not Available
- Patents
- Not Available
Properties
- State
- Solid
- Experimental Properties
- Not Available
- Predicted Properties
Property Value Source Water Solubility 0.00328 mg/mL ALOGPS logP 5 ALOGPS logP 4.94 Chemaxon logS -5.3 ALOGPS pKa (Strongest Acidic) 5.15 Chemaxon pKa (Strongest Basic) -3.9 Chemaxon Physiological Charge -1 Chemaxon Hydrogen Acceptor Count 9 Chemaxon Hydrogen Donor Count 5 Chemaxon Polar Surface Area 185.87 Å2 Chemaxon Rotatable Bond Count 10 Chemaxon Refractivity 179.79 m3·mol-1 Chemaxon Polarizability 72.3 Å3 Chemaxon Number of Rings 5 Chemaxon Bioavailability 1 Chemaxon Rule of Five No Chemaxon Ghose Filter No Chemaxon Veber's Rule No Chemaxon MDDR-like Rule Yes Chemaxon - Predicted ADMET Features
Property Value Probability Human Intestinal Absorption + 0.6834 Blood Brain Barrier - 0.914 Caco-2 permeable - 0.6412 P-glycoprotein substrate Substrate 0.7412 P-glycoprotein inhibitor I Non-inhibitor 0.6718 P-glycoprotein inhibitor II Non-inhibitor 0.7421 Renal organic cation transporter Non-inhibitor 0.9457 CYP450 2C9 substrate Non-substrate 0.8504 CYP450 2D6 substrate Non-substrate 0.8459 CYP450 3A4 substrate Substrate 0.6519 CYP450 1A2 substrate Non-inhibitor 0.7642 CYP450 2C9 inhibitor Non-inhibitor 0.5979 CYP450 2D6 inhibitor Non-inhibitor 0.8654 CYP450 2C19 inhibitor Non-inhibitor 0.6369 CYP450 3A4 inhibitor Non-inhibitor 0.818 CYP450 inhibitory promiscuity High CYP Inhibitory Promiscuity 0.6217 Ames test Non AMES toxic 0.649 Carcinogenicity Non-carcinogens 0.9188 Biodegradation Not ready biodegradable 1.0 Rat acute toxicity 2.5298 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9931 hERG inhibition (predictor II) Non-inhibitor 0.8237
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
- Chromatographic Properties
Collision Cross Sections (CCS)
Adduct CCS Value (Å2) Source type Source [M-H]- 298.8659873 predictedDarkChem Lite v0.1.0 [M-H]- 235.2454 predictedDeepCCS 1.0 (2019) [M+H]+ 298.7599873 predictedDarkChem Lite v0.1.0 [M+H]+ 237.54402 predictedDeepCCS 1.0 (2019) [M+Na]+ 298.6819873 predictedDarkChem Lite v0.1.0 [M+Na]+ 243.45654 predictedDeepCCS 1.0 (2019)
Targets
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- Kind
- Protein
- Organism
- Humans
- Pharmacological action
- Yes
- Actions
- Inhibitor
- General Function
- Key decatenating enzyme that alters DNA topology by binding to two double-stranded DNA molecules, generating a double-stranded break in one of the strands, passing the intact strand through the broken strand, and religating the broken strand. Plays a role in B-cell differentiation
- Specific Function
- ATP binding
- Gene Name
- TOP2B
- Uniprot ID
- Q02880
- Uniprot Name
- DNA topoisomerase 2-beta
- Molecular Weight
- 183265.825 Da
References
- Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y, Wang S, Qiu Y, Chen Y, Zhu F: TTD: Therapeutic Target Database describing target druggability information. Nucleic Acids Res. 2024 Jan 5;52(D1):D1465-D1477. doi: 10.1093/nar/gkad751. [Article]
- Kind
- Protein
- Organism
- Humans
- Pharmacological action
- Yes
- Actions
- Inhibitor
- General Function
- Key decatenating enzyme that alters DNA topology by binding to two double-stranded DNA molecules, generating a double-stranded break in one of the strands, passing the intact strand through the broken strand, and religating the broken strand (PubMed:17567603, PubMed:18790802, PubMed:22013166, PubMed:22323612). May play a role in regulating the period length of BMAL1 transcriptional oscillation (By similarity)
- Specific Function
- ATP binding
- Gene Name
- TOP2A
- Uniprot ID
- P11388
- Uniprot Name
- DNA topoisomerase 2-alpha
- Molecular Weight
- 174383.88 Da
References
- Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y, Wang S, Qiu Y, Chen Y, Zhu F: TTD: Therapeutic Target Database describing target druggability information. Nucleic Acids Res. 2024 Jan 5;52(D1):D1465-D1477. doi: 10.1093/nar/gkad751. [Article]
- Kind
- Protein
- Organism
- Escherichia coli (strain K12)
- Pharmacological action
- Unknown
- General Function
- DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner to maintain chromosomes in an underwound state (PubMed:12051842, PubMed:12051843, PubMed:1323022, PubMed:18642932, PubMed:186775, PubMed:19060136, PubMed:19965760, PubMed:20356737, PubMed:20675723, PubMed:22457353, PubMed:23294697, PubMed:23352267, PubMed:24386374, PubMed:25202966, PubMed:25849408, PubMed:3031051, PubMed:7811004, PubMed:8248233, PubMed:8621650, PubMed:9657678). This makes better substrates for topoisomerase 4 (ParC and ParE) which is the main enzyme that unlinks newly replicated chromosomes in E.coli (PubMed:9334322). Gyrase catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:22457352). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:337300). E.coli gyrase has higher supercoiling activity than other characterized bacterial gyrases; at comparable concentrations E.coli gyrase introduces more supercoils faster than M.tuberculosis gyrase, while M.tuberculosis gyrase has higher decatenation than supercoiling activity compared to E.coli (PubMed:22457352). E.coli makes 15% more negative supercoils in pBR322 plasmid DNA than S.typhimurium; the S.typhimurium GyrB subunit is toxic in E.coli, while the E.coli copy can be expressed in S.typhimurium even though the 2 subunits have 777/804 residues identical (PubMed:17400739). The enzymatic differences between E.coli gyrase and topoisomerase IV are largely due to the GyrA C-terminal domain (approximately residues 524-841) and specifically the GyrA-box (PubMed:16332690, PubMed:8962066).
- Specific Function
- ATP binding
- Gene Name
- gyrB
- Uniprot ID
- P0AES6
- Uniprot Name
- DNA gyrase subunit B
- Molecular Weight
- 89949.195 Da
References
- Tsai FT, Singh OM, Skarzynski T, Wonacott AJ, Weston S, Tucker A, Pauptit RA, Breeze AL, Poyser JP, O'Brien R, Ladbury JE, Wigley DB: The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins. 1997 May;28(1):41-52. [Article]
- Hooper DC, Wolfson JS, McHugh GL, Winters MB, Swartz MN: Effects of novobiocin, coumermycin A1, clorobiocin, and their analogs on Escherichia coli DNA gyrase and bacterial growth. Antimicrob Agents Chemother. 1982 Oct;22(4):662-71. [Article]
Drug created at June 13, 2005 13:24 / Updated at August 26, 2024 19:22