Similarity search finds compounds in ChEMBL that are structurally similar to a query molecule, ranked by Tanimoto coefficient — useful for expanding SAR around a known active or hopping to new scaffolds. The threshold you ask for most affects the result: high values (≥85%) return few, near-identical hits, while lower values (50–70%) surface more diverse scaffold-hopping candidates.

ChEMBL Similarity Search

Find compounds in ChEMBL that are structurally similar to a query molecule, ranked by Tanimoto similarity.

What you can ask for

Filter	Default	Limits
Query molecule	Required	One SMILES string per search (not a comma-separated list), up to 1000 characters
Similarity threshold	70%	Minimum Tanimoto similarity, 40-100%
Number of results	20	Up to 100 per search

Tanimoto Coefficient

The Tanimoto coefficient measures structural similarity between molecules based on molecular fingerprints. The threshold is a percentage from 40 to 100:

Threshold	Interpretation
100%	Identical fingerprints
≥85%	Very high similarity (likely same scaffold)
70–85%	High similarity (good for SAR expansion)
50–70%	Moderate similarity (scaffold hopping candidates)
<50%	Low similarity (different chemical series) — thresholds below the 40% floor are rejected

Scope

Similarity search finds molecules that are globally similar by Tanimoto fingerprint comparison. There is no separate ChEMBL substructure-search tool on the platform — for a specific chemical motif, run this similarity search at a lower threshold (50-60%) to surface a broader candidate set, then filter the results by hand.

Chat Usage

Example Prompts

"Find compounds similar to aspirin in ChEMBL with Tanimoto > 0.8"
"Search ChEMBL for analogs of CC(=O)Oc1ccccc1C(=O)O above 0.7 similarity"

Workflow Chaining

Feeds into: ADMET screening, DiffDock, Compound Passport
Accepts from: PubChem (compound SMILES), REINVENT (generated molecules)

ChEMBL similarity search