Chembl MCP Server

@cyanheads/chembl-mcp-server Link compounds to protein targets, rank bioactivity (IC50/Ki/EC50), and look up drug mechanisms and indications over ChEMBL via MCP. STDIO or Streamable HTTP. 7 Tools (+1 opt-in) • 2 Resources

Public Hosted Server: https://chembl.caseyjhand.com/mcp

Overview

Drug-discovery data from ChEMBL (EBI): the curated link between compounds, protein targets, and measured bioactivity (IC50/Ki/EC50), plus drug mechanisms and indications. Search compounds by name, ID, or structure, resolve targets, and rank the most potent measurements.

Tools

Resources

All resource data is also reachable via the tools, so tool-only MCP clients lose nothing. There are no prompts — the canonical workflows are short tool chains an agent composes directly, and the cross-server chain guidance ships as server-level instructions instead.

Skills

Capability reference

chembl_search_molecules tool

• Default search_type=name matches drug names, synonyms, ChEMBL IDs, and InChIKeys in one query; a query that is exactly a ChEMBL ID or InChIKey routes to ChEMBL's single-record lookup instead of the fuzzy text index (totalCount: 1)
• Structure search via search_type: exact, similarity (Tanimoto ≥ similarity_threshold, integer 40–100, default 70), or substructure — supply structure as a SMILES; max_phase_min (name search only) restricts to compounds at or above a max clinical phase. A SMILES ChEMBL cannot parse fails a similarity or substructure search on the first request as invalid_structure, not as an outage
• Every row carries max_phase, MW, AlogP, Lipinski rule-of-five violations, and QED; only search_type=similarity results carry a Tanimoto similarity percent — absent, not null, on other modes
• Every row also carries parent_chembl_id, the parent of its family: ERLOTINIB HYDROCHLORIDE (CHEMBL1079742) names CHEMBL553, and a compound with no recorded hierarchy names itself. A salt can rank ahead of its parent while holding a small share of the family's measurements
• Paginated via nextCursor / cursor, omitted (not null) on the last page — redeem a cursor with the same filters that minted it; a limit above 100 is served at 100, with a notice
• ChEMBL stops counting and paging a name search at 10,000 matches and a substructure search at 30,000; a total at that ceiling comes back as totalCountCapped: true with a notice that at least that many match and the rest are out of reach — narrow the query to get under it
• Chain molecule_chembl_id into chembl_get_bioactivities or chembl_get_drug_info

chembl_get_bioactivities tool

• Supply at least one of molecule_chembl_id or target_chembl_id; supplying both narrows to that compound–target pair — neither is a missing_filter error
• include_alternate_forms: true widens molecule_chembl_id to its family — the parent and every salt and other alternate form ChEMBL files under it (imatinib CHEMBL941: 4,878 measurements alone, 5,802 across its forms); a salt's ID reaches the same family, and each row keeps the form it was measured on. The count, both views, cursor pages, and the spill read the same family; re-send the flag with a cursor. Without molecule_chembl_id the flag is an alternate_forms_without_molecule error
• IDs are matched in canonical form: "chembl941" and " CHEMBL941 " read as CHEMBL941, and a value that is no ChEMBL ID ("imatinib") fails with -32602 before any request, routing to the search tools — for molecule_chembl_id, when include_alternate_forms is off and the value goes straight to the filter
• Filter by standard_type (IC50/Ki/EC50/…), pchembl_value_min, assay_type, organism, and variant; ranked on pchembl_value — comparable only within one standard_type
• assay_type takes a code (B / F / A / T / P / U) or ChEMBL's name for it (binding, ADMET, …) in any case. standard_type matches exactly, case included — ChEMBL holds distinct types that differ only by case (Kd / KD) — and when nothing matches, the notice names a case variant ChEMBL records under the same filters ("ic50" → IC50)
• variant separates wild-type from mutant potency: "wild_type" keeps the measurements that record no variant, and any other value matches the whole recorded variant case-insensitively ("T315I", "F508del", "L858R,T790M" in ChEMBL's order, "UNDEFINED MUTATION") — "L858R" alone does not match "L858R,T790M"
• Each row carries activity_comment (e.g. Not Active, often the only result when no value was measured) and data_validity_comment (e.g. Outside typical range), the assay's assay_variant_mutation and assay_variant_accession, and the source document_chembl_id and document_year for citation
• potency_view selects potency_ranked (default, measurements with a derivable pchembl_value) or null_potency (the excluded rows); pchembl_value_min with null_potency is a contradictory_potency_filter error, and totalCount spans both views
• Numerics are coerced to number | null at the service boundary — a missing potency reads as null, never 0
• Large sets spill to a DataCanvas table per view (bioactivities / bioactivities_null_potency); the canvas is on by default, and CANVAS_PROVIDER_TYPE=none turns it off
• The spill fetches its pages CHEMBL_MAX_CONCURRENT_PAGES at a time (default 4) and stays inside a row cap, CHEMBL_MAX_SPILL_ROWS (default 50,000), and a time budget, CHEMBL_SPILL_DEADLINE_MS (default 45 s). When either bound stops it short of the view, the response reports truncated: true, staged_row_count, and truncated_by (row_cap or time_budget)
• The inline preview is always capped at limit (default 25) regardless of spill status; a limit above 1,000 is served at 1,000, with a notice
• A canvas is minted only when the view spills, so an inline fit holds no canvas; pass the returned canvas_id back and each later non-cursor call re-stages that view's table with its own rows — even when they fit inline or none match — replacing the prior rows, while the other view's table stays put. A spill replaces the table only once it succeeds, so one that fails or is cancelled leaves the prior rows. At the per-tenant canvas cap, a spill without canvas_id fails as canvas_capacity_exhausted
• Whenever a call stages nothing (the canvas is disabled, or the view fit inline with no canvas_id), the view comes back a page at a time via nextCursor / cursor, omitted (not null) on the last page — redeem a cursor with the same filters and potency_view that minted it; a cursor page is served inline and never staged, even with the canvas enabled

chembl_search_targets tool

• Supply at least one of accession (UniProt, e.g. P00533), gene_symbol, or query (free-text); narrow with organism and target_type — none supplied is a missing_input error
• A UniProt accession is the most precise input — chain it from a uniprot/protein server. accession and target_type are matched uppercase, the form ChEMBL records ("p00533" reads as P00533, "single protein" as SINGLE PROTEIN); gene_symbol and organism already match case-insensitively
• Each row carries target type, organism, and component UniProt accessions + gene symbols, flattened from ChEMBL's nested component synonyms
• Paginated via nextCursor / cursor, the same contract as chembl_search_molecules, limit clamp included
• Chain target_chembl_id into chembl_get_bioactivities

chembl_get_drug_info tool

• Supply molecule_chembl_id (any case) or the molecule's standard InChIKey; ret