From August 18th 2026, GtoPdb will require users to register to use the website. Please see our blog post for more information.

compound 3 [PMID: 24440480]   Click here for help

GtoPdb Ligand ID: 8682

Compound class: Synthetic organic
Comment: Compound 3 is reported as an irreversible pan-protein-arginine deiminase (PADI) inhibitor [1]. Compound 3 is an analogue fragment of streptonigrin.
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 5
Hydrogen bond donors 1
Rotatable bonds 1
Topological polar surface area 85.94
Molecular weight 251.07
XLogP 1.08
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
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 NC1=CC(=O)c2c(C1=O)nc(cc2)c1ccccn1
Isomeric SMILES NC1=CC(=O)c2c(C1=O)nc(cc2)c1ccccn1
InChI InChI=1S/C14H9N3O2/c15-9-7-12(18)8-4-5-11(17-13(8)14(9)19)10-3-1-2-6-16-10/h1-7H,15H2
InChI Key UMMNKCUSQIKSGP-UHFFFAOYSA-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
The authors provide inhibition values as Kinact/KI, which is appropriate for quantifying irreversible enzyme inhibition. NB click on the down arrow at the end of the row in the table below to reveal the rate constant.
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
peptidyl arginine deiminase 4 N/A Inhibitor Irreversible inhibition - - - 1
⤷ [1]
Description: Kinact/KI = 5.7x103 M-1 min-1
peptidyl arginine deiminase 3 N/A Inhibitor Irreversible inhibition - - - 1
⤷ [1]
Description: Kinact/KI = 1.8x103 M-1 min-1