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
Classification Click here for help
Compound class Natural product
Approved drug? Yes (FDA (1964))
Withdrawn drug? Yes
IUPAC Name Click here for help
[(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate
International Nonproprietary Names Click here for help
INN number INN
575 novobiocin
Synonyms Click here for help
Albamycin® | cardelmycin | cathomycin | PA 93 | streptonivicin
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Novobiocin
Other databases
CAS Registry No. 303-81-1 (source: Scifinder)
ChEBI CHEBI:28368
ChEMBL Ligand CHEMBL36506
DrugBank Ligand DB01051
DrugCentral Ligand 1974
GtoPdb PubChem SID 464244162
PubChem CID 54675769
RCSB PDB Ligand NOV
Search Google for chemical match using the InChIKey YJQPYGGHQPGBLI-KGSXXDOSSA-N
Search Google for chemicals with the same backbone YJQPYGGHQPGBLI
Search PubMed clinical trials novobiocin
Search PubMed titles novobiocin
Search PubMed titles/abstracts novobiocin
UniChem Compound Search for chemical match using the InChIKey YJQPYGGHQPGBLI-KGSXXDOSSA-N
UniChem Connectivity Search for chemical match using the InChIKey YJQPYGGHQPGBLI-KGSXXDOSSA-N
Wikipedia Novobiocin