novobiocin   Click here for help

GtoPdb Ligand ID: 12021

Synonyms: Albamycin® | cardelmycin | cathomycin | PA 93 | streptonivicin
Approved drug PDB Ligand
novobiocin is an approved drug (FDA (1964))
Compound class: Natural product
Comment: Novobiocin was originally isolated from the actinomycete Streptomyces niveus and belongs to the aminocoumarins, a class of compounds characterized by a 3-amino-4,7-dihydroxycoumarin ring. It is effective against Gram-positive bacteria but has limited activity against Gram-negative pathogens.
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 8
Hydrogen bond donors 5
Rotatable bonds 10
Topological polar surface area 200.01
Molecular weight 612.23
XLogP 4.49
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES CO[C@@H]1[C@@H](OC(=O)N)[C@@H](O)[C@@H](OC1(C)C)Oc1ccc2c(c1C)oc(=O)c(c2O)NC(=O)c1ccc(c(c1)CC=C(C)C)O
Isomeric SMILES Cc1c(ccc2c1oc(=O)c(c2O)NC(=O)c1cc(c(cc1)O)CC=C(C)C)O[C@H]1[C@@H]([C@@H]([C@H](C(O1)(C)C)OC)OC(=O)N)O
InChI InChI=1S/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1
InChI Key YJQPYGGHQPGBLI-KGSXXDOSSA-N
Bioactivity Comments
MIC90 for antibacterial activity against strains of methicillin-resistant Staphylococcus aureus (MRSA) is 0.25 μg/ml in vitro [4].
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
DNA gyrase subunit B E.coli Inhibitor Competitive 7.1 pIC50 - 1
⤷ pIC50 7.1 (IC50 8x10-8 M) [1]
Description: DNA gyrase supercoiling assay
Targets where the ligand is described in the comment field
Target Comment
DNA gyrase DNA gyrase is a type II DNA topoisomerase [2] and one of two enzymes of this subclass found in bacteria, the other being DNA topoisomerase 4. DNA gyrase introduces negative supercoils in closed circular double-stranded DNA in an ATP-dependent manner.
This enzyme is the clinically-validated target for a number of antibacterial drug classes, including the aminocoumarins such as novobiocin and fluoroquinolones such as moxifloxacin, levofloxacin, ciprofloxacin and ofloxacin.