GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

erucamide   Click here for help

GtoPdb Ligand ID: 13954

PDB Ligand
Compound class: Natural product
Comment: Erucamide is a phytoalexin with promising anti-virulence activity against Gram-negative bacteria [2]. Functionally it is an inhibitor of the type III secretion system (T3SS) [3], one of the main pathogenicity factors of Gram-negative bacteria [1].
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 2
Hydrogen bond donors 1
Rotatable bonds 19
Topological polar surface area 43.09
Molecular weight 337.58
XLogP 9.74
No. Lipinski's rules broken 2

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 CCCCCCCC/C=C\CCCCCCCCCCCC(=O)N
Isomeric SMILES CCCCCCCC/C=C\CCCCCCCCCCCC(=O)N
InChI InChI=1S/C22H43NO/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22(23)24/h9-10H,2-8,11-21H2,1H3,(H2,23,24)/b10-9-
InChI Key UAUDZVJPLUQNMU-KTKRTIGZSA-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. Deng W, Marshall NC, Rowland JL, McCoy JM, Worrall LJ, Santos AS, Strynadka NCJ, Finlay BB. (2017)
Assembly, structure, function and regulation of type III secretion systems.
Nat Rev Microbiol, 15 (6): 323-337. [PMID:28392566]
2. Miao P, Wang H, Wang W, Wang Z, Ke H, Cheng H, Ni J, Liang J, Yao YF, Wang J et al.. (2025)
A widespread plant defense compound disarms bacterial type III injectisome assembly.
Science, 387 (6737): eads0377. [PMID:40014714]
3. Zigangirova NA, Zayakin ES, Kapotina LN, Kost EA, Didenko LV, Davydova DY, Rumyanceva JP, Gintsburg AL. (2012)
Development of Chlamydial Type III Secretion System Inhibitors for Suppression of Acute and Chronic Forms of Chlamydial Infection.
Acta Naturae, 4 (2): 87-97. [PMID:22880162]