difficidin   Click here for help

GtoPdb Ligand ID: 11062

Compound class: Natural product
Comment: Difficidin is a macrocyclic polyene lactone phosphate ester originally isolated from Bacillus subtilis. It has potent antibacterial activity in vitro against a broad spectrum of aerobic and anaerobic organisms [1].
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 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 6
Hydrogen bond donors 2
Rotatable bonds 6
Topological polar surface area 102.87
Molecular weight 544.3
XLogP 6.54
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
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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 C=C/C=C(/CCC1C/C=C/C=C(\C)/C(CCC/C=C\C=C/C=C/CC(C(=C)CC(=O)O1)C)OP(=O)(O)O)\C
Isomeric SMILES C=C/C=C(/CCC1C/C=C/C=C(\C)/C(CCC/C=C\C=C/C=C/CC(C(=C)CC(=O)O1)C)OP(=O)(O)O)\C
InChI InChI=1S/C31H45O6P/c1-6-17-25(2)22-23-29-20-16-15-19-27(4)30(37-38(33,34)35)21-14-12-10-8-7-9-11-13-18-26(3)28(5)24-31(32)36-29/h6-11,13,15-17,19,26,29-30H,1,5,12,14,18,20-24H2,2-4H3,(H2,33,34,35)/b9-7-,10-8-,13-11+,16-15+,25-17+,27-19+
InChI Key ZUWUQYGHRURWCL-XUIVTPDHSA-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/)
Bioactivity Comments
MICs for antibacterial activity in vitro against aerobic spp. range from 0.5-16 μg/ml, with the exception of Streptococcus faecalis (>128 μg/ml) [1]. Difficidin also demonstrates potent activity against anaerobes including strains of Clostridium difficile (0.06-0.125 μg/ml).