Clorobiocin

Identification

Name
Clorobiocin
Accession Number
DB03966  (EXPT00847)
Type
Small Molecule
Groups
Experimental
Description

Clorobiocin is an aminocoumarin antibiotic, similar to novobiocin and coumermycin A1.

Structure
Thumb
Synonyms
  • Chlorobiocin
Categories
UNII
Not Available
CAS number
39868-96-7
Weight
Average: 697.128
Monoisotopic: 696.208587743
Chemical Formula
C35H37ClN2O11
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
[H][C@]1(O)[C@]([H])(OC2=C(Cl)C3=C(C=C2)C(O)=C(NC(=O)C2=CC=C(O)C(CC=C(C)C)=C2)C(=O)O3)OC(C)(C)[C@]([H])(OC)[C@@]1([H])OC(=O)C1=CC=C(C)N1

Pharmacology

Indication
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UDNA gyrase subunit BNot AvailableEscherichia 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
Toxicity
Not Available
Affected organisms
  • Enteric bacteria and other eubacteria
Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
  1. 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. [PubMed:9144789]
  2. Cejka K, Holubova I, Hubacek J: Curing effect of clorobiocin on Escherichia coli plasmids. Mol Gen Genet. 1982;186(1):153-5. [PubMed:7050623]
External Links
KEGG Compound
C12032
PubChem Compound
54706138
PubChem Substance
46505267
ChemSpider
21256053
BindingDB
50330317
ChEMBL
CHEMBL303984
HET
CBN
Wikipedia
Clorobiocin
PDB Entries
1kzn

Clinical Trials

Clinical Trials
Not Available

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
PropertyValueSource
Water Solubility0.00328 mg/mLALOGPS
logP5ALOGPS
logP4.94ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)6.51ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area185.87 Å2ChemAxon
Rotatable Bond Count10ChemAxon
Refractivity179.79 m3·mol-1ChemAxon
Polarizability73.19 Å3ChemAxon
Number of Rings5ChemAxon
Bioavailability1ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.6834
Blood Brain Barrier-0.914
Caco-2 permeable-0.6412
P-glycoprotein substrateSubstrate0.7412
P-glycoprotein inhibitor INon-inhibitor0.6718
P-glycoprotein inhibitor IINon-inhibitor0.7421
Renal organic cation transporterNon-inhibitor0.9457
CYP450 2C9 substrateNon-substrate0.8504
CYP450 2D6 substrateNon-substrate0.8459
CYP450 3A4 substrateSubstrate0.6519
CYP450 1A2 substrateNon-inhibitor0.7642
CYP450 2C9 inhibitorNon-inhibitor0.5979
CYP450 2D6 inhibitorNon-inhibitor0.8654
CYP450 2C19 inhibitorNon-inhibitor0.6369
CYP450 3A4 inhibitorNon-inhibitor0.818
CYP450 inhibitory promiscuityHigh CYP Inhibitory Promiscuity0.6217
Ames testNon AMES toxic0.649
CarcinogenicityNon-carcinogens0.9188
BiodegradationNot ready biodegradable1.0
Rat acute toxicity2.5298 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9931
hERG inhibition (predictor II)Non-inhibitor0.8237
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSNot Available

Taxonomy

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
Coumarin o-glycoside / Coumarin-7-o-glycoside / Phenolic glycoside / 4-hydroxycoumarin / Hydroxycoumarin / Hexose monosaccharide / O-glycosyl compound / Glycosyl compound / Benzopyran / 1-benzopyran
show 42 more
Molecular Framework
Aromatic heteropolycyclic compounds
External Descriptors
Not Available

Targets

Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Magnesium ion binding
Specific Function
DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, inc...
Gene Name
gyrB
Uniprot ID
P0AES6
Uniprot Name
DNA gyrase subunit B
Molecular Weight
89949.195 Da
References
  1. 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. [PubMed:9144789]
  2. 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. [PubMed:6295263]

Drug created on June 13, 2005 07:24 / Updated on October 01, 2018 13:43