NAV

Clorobiocin

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
3D
Similar Structures
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
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Pharmacology

Indication

Not Available

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Contraindications & Blackbox Warnings
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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

Adverse Effects
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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.
DrugInteraction
Integrate drug-drug
interactions in your software
AcetohexamideThe therapeutic efficacy of Acetohexamide can be increased when used in combination with Clorobiocin.
ChlorpropamideThe therapeutic efficacy of Chlorpropamide can be increased when used in combination with Clorobiocin.
DexmethylphenidateThe serum concentration of the active metabolites of Clorobiocin can be increased when Clorobiocin is used in combination with Dexmethylphenidate.
DiazoxideThe serum concentration of Clorobiocin can be increased when it is combined with Diazoxide.
DoxycyclineThe 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
  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. [Article]
  2. Cejka K, Holubova I, Hubacek J: Curing effect of clorobiocin on Escherichia coli plasmids. Mol Gen Genet. 1982;186(1):153-5. [Article]
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
PhaseStatusPurposeConditionsCount

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)5.15Chemaxon
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
Polarizability72.3 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/MSsplash10-052b-2410129000-a5ba16a3e0ed99be748e
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0002-0100009000-af07f53bdf39a804c53e
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-001i-9410212000-3bcdf917c1ddb05ac350
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-05fr-1101293000-b669b207525c821545b1
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-001r-8920208000-6d7db91bd3cdbf85e86a
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-9100002000-87c9e4a955c4b6b65bf4
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-298.8659873
predicted
DarkChem Lite v0.1.0
[M-H]-235.2454
predicted
DeepCCS 1.0 (2019)
[M+H]+298.7599873
predicted
DarkChem Lite v0.1.0
[M+H]+237.54402
predicted
DeepCCS 1.0 (2019)
[M+Na]+298.6819873
predicted
DarkChem Lite v0.1.0
[M+Na]+243.45654
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. DNA gyrase subunit B
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. [Article]
  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. [Article]

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52