novclobiocin 101   Click here for help

GtoPdb Ligand ID: 12131

Compound class: Natural product
Comment: Novclobiocin 101 is an aminocoumarin antibacterial compound and a structural analogue of clorobiocin [2].
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
Hydrogen bond acceptors 7
Hydrogen bond donors 5
Rotatable bonds 11
Topological polar surface area 189.78
Molecular weight 662.25
XLogP 5.91
No. Lipinski's rules broken 1

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
Click here for help

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/)

✖
Canonical SMILES CO[C@@H]1[C@@H](OC(=O)c2ccc([nH]2)C)[C@@H](O)[C@@H](OC1(C)C)Oc1ccc2c(c1)oc(=O)c(c2O)NC(=O)c1ccc(c(c1)CC=C(C)C)O
Isomeric SMILES Cc1ccc([nH]1)C(=O)O[C@H]1[C@H]([C@@H](OC([C@@H]1OC)(C)C)Oc1cc2c(cc1)c(c(c(=O)o2)NC(=O)c1cc(c(cc1)O)CC=C(C)C)O)O
InChI InChI=1S/C35H38N2O11/c1-17(2)7-9-19-15-20(10-14-24(19)38)31(41)37-26-27(39)22-12-11-21(16-25(22)46-33(26)43)45-34-28(40)29(30(44-6)35(4,5)48-34)47-32(42)23-13-8-18(3)36-23/h7-8,10-16,28-30,34,36,38-40H,9H2,1-6H3,(H,37,41)/t28-,29+,30-,34-/m1/s1
InChI Key GMMYCBAAMDJSHV-YQQRZDPSSA-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/)
No information available.
Mechanism Of Action and Pharmacodynamic Effects Click here for help
Novclobiocin 101 is a potent inhibitor of DNA gyrase, a type II DNA topoisomerase that catalyzes the negative supercoiling of DNA and is essential in all bacteria but absent from higher eukaryotes [1,3].