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chembl_​get_​small_​molecule_​structures

<p>Tool name: <strong>chembl_get_small_molecule_structures</strong></p><p>Description: Enriches a table of ChEMBL compounds with structural identifiers (SMILES and InChIKey). Accepts a KNIME table containing a chembl_id column and returns the same table with canonical_smiles, standard_inchi_key, and molecule_type appended. Only small molecules will have structural identifiers; biologics and cell therapies will have NULL values in those columns.</p>

Tool name: chembl_get_small_molecule_structures

Description: Enriches a table of ChEMBL compounds with structural identifiers (SMILES and InChIKey). Accepts a KNIME table containing a chembl_id column and returns the same table with canonical_smiles, standard_inchi_key, and molecule_type appended. Only small molecules will have structural identifiers; biologics and cell therapies will have NULL values in those columns.

Adjust for connection to your ChEMBL PostgreSQL database.

connect toChEMBL
PostgreSQL Connector
Merge Variables
Secrets Retriever
GroupBy
String Manipulation (Variable)
Table Row to Variable
Table Reader
Table Row to Variable
DB Query Reader
Molecule Type Cast
Table Row to Variable
Collection to String
Math Formula (Variable)
Variable to Table Row
DB Connection Closer
GroupBy
Workflow Input
KNIME Hub Authenticator
Workflow Output
Joiner
Tool Message Output
GroupBy

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: Tugrul Kaynak
Created at: 2026-03-27
On NodePit since: 2026-05-06
Last update: 2026-05-06
Created with KNIME version: v5.11.0

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