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

novobiocin is commercially available from our sponsors

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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Click here for structure editor
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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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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

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Alt S, Mitchenall LA, Maxwell A, Heide L. (2011)
Inhibition of DNA gyrase and DNA topoisomerase IV of Staphylococcus aureus and Escherichia coli by aminocoumarin antibiotics.
J Antimicrob Chemother, 66 (9): 2061-9. [PMID:21693461]
2. Gellert M, Mizuuchi K, O'Dea MH, Nash HA. (1976)
DNA gyrase: an enzyme that introduces superhelical turns into DNA.
Proc Natl Acad Sci U S A, 73 (11): 3872-6. [PMID:186775]
3. Gellert M, O'Dea MH, Itoh T, Tomizawa J. (1976)
Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase.
Proc Natl Acad Sci U S A, 73 (12): 4474-8. [PMID:794878]
4. Walsh TJ, Hansen SL, Tatem BA, Auger F, Standiford HC. (1985)
Activity of novobiocin against methicillin-resistant Staphylococcus aureus.
J Antimicrob Chemother, 15 (4): 435-40. [PMID:3847438]