@cyanheads/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

Tools

Eight tools — five for the ChEMBL compound/target/bioactivity surface, plus three for SQL analytics over the DuckDB-backed canvas that chembl_get_bioactivities spills to (the third is opt-in):

Tool	Description
chembl_search_molecules	Find compounds by name / ChEMBL ID / InChIKey, or run a structure search (exact | similarity | substructure) from a SMILES.
chembl_get_bioactivities	The flagship compound↔target bridge: bioactivity measurements for a molecule or a target, ranked on pchembl_value. Large sets spill to a canvas.
chembl_search_targets	Resolve a protein / gene symbol / UniProt accession to the ChEMBL target ID chembl_get_bioactivities needs.
chembl_get_drug_info	Drug pharmacology — mechanism(s) of action, molecular target(s), action type, first-approval year, and clinical indications.
chembl_get_assay	Assay provenance behind a bioactivity row — type, target, organism, and ChEMBL's 1–9 confidence score.
chembl_dataframe_query	Run a read-only SQL SELECT over the bioactivity rows spilled to a canvas — rank, group, dedupe, aggregate across the full set.
chembl_dataframe_describe	List the tables and columns staged on a canvas, so you can write correct SQL before querying.
chembl_dataframe_drop	Drop a named staged table from a canvas. Opt-in via CHEMBL_DATAFRAME_DROP_ENABLED=true — absent from tools/list when off, since TTL already reclaims staged tables.

chembl_search_molecules

The discovery entry point for compounds.

• Default search_type=name matches drug names, synonyms, ChEMBL IDs, and InChIKeys in one query
• Structure search via search_type: exact (exact match), similarity (Tanimoto ≥ threshold), or substructure (contains the query structure) — supply structure as a SMILES
• similarity_threshold is an integer 40–100 (default 70; ChEMBL rejects values below 40)
• max_phase_min restricts name searches to compounds at or above a max clinical phase (e.g. 4 for marketed drugs only)
• Every row carries max_phase — the cheap druggability signal (4 = marketed, 0 = research) — plus MW, AlogP, Lipinski rule-of-five violations, and QED; structure searches also return a Tanimoto similarity percent
• Chain molecule_chembl_id into chembl_get_bioactivities or chembl_get_drug_info

chembl_get_bioactivities

The flagship tool and the reason the server exists — the curated compound↔target↔assay link.

• Supply exactly one of molecule_chembl_id (target deconvolution / selectivity) or target_chembl_id (lead finding); both or neither is a missing_filter error
• Filter by standard_type (IC50 / Ki / EC50 / …), minimum potency pchembl_value_min, assay_type, and organism; rows are ranked on pchembl_value (−log10 molar potency)
• Ranking trap: pchembl_value is comparable only within one standard_type — set the filter, because mixing IC50 and Ki is a scientific error
• Numerics are coerced from upstream JSON strings to number | null at the service boundary — a missing potency reads as null, never 0
• A popular target carries tens of thousands of measurements: when the set exceeds the inline preview it spills to a DataCanvas table (bioactivities) you SQL with chembl_dataframe_query for honest aggregates across the full set, while the inline preview answers the immediate question
• Spilling requires CANVAS_PROVIDER_TYPE=duckdb; without it the preview is the full inlined set (capped at limit)
• The optional canvas_id reuses an existing canvas, but the bioactivities table is always re-registered — a second query replaces the prior rows on that canvas rather than appending; omit canvas_id to mint a fresh one

chembl_search_targets

Resolve a protein into the ChEMBL target ID downstream tools need.

• Supply at least one of accession (UniProt, e.g. P00533), gene_symbol (e.g. EGFR), or query (free-text name); narrow further with organism and target_type
• A UniProt accession is the most precise input — chain it from a uniprot / protein server
• Each row carries the target type, organism, and component UniProt accessions + gene symbols (flattened from ChEMBL's nested component synonyms)
• Chain target_chembl_id into chembl_get_bioactivities

chembl_get_drug_info

Drug pharmacology for a molecule — distinct from the openfda server's label / adverse-event view.

• Supply molecule_chembl_id (from chembl_search_molecules)
• Returns mechanism(s) of action, the molecular target(s), action type (inhibitor / agonist / …), first-approval year, and clinical indications with the max phase reached for each
• Composed from molecule + mechanisms + indications with Promise.allSettled, so a missing mechanism or indication list degrades to an empty array rather than failing the call
• A mechanism's target_chembl_id chains into chembl_get_bioactivities for compounds hitting the same target

chembl_get_assay

Assay provenance behind a bioactivity row — call it to judge whether two measurements are comparable before ranking them together.

• Supply assay_chembl_id from a chembl_get_bioactivities row
• Returns the description, assay type (binding / functional / ADMET / toxicity), the target it measures, organism, and ChEMBL's 1–9 confidence score (9 = direct assay on the protein target, lower = homologous or indirect)

chembl_dataframe_query / chembl_dataframe_describe / chembl_dataframe_drop

In-conversation SQL analytics over the bioactivities table that chembl_get_bioactivities spills to a DuckDB-backed canvas. When a query spills, the tool returns a canvas_id; pass it to chembl_dataframe_query for ranking, grouping, deduplication, and aggregation across the full set — standard DuckDB SQL.

• Read-only. chembl_dataframe_query accepts a single SELECT; writes, DDL, and non-SELECT statements are rejected by the framework SQL gate. Reference the staged table by the name chembl_get_bioactivities returned (bioactivities), and discover its columns with chembl_dataframe_describe first.
• The spilled table holds the full Activity row — 18 columns including the normalized standard_* / pchembl_value fields (rank on these) and the raw upstream type / value / units / relation (audit only). Compute aggregates here, never over the inline preview.
• chembl_dataframe_drop is the only destructive tool and is opt-in (CHEMBL_DATAFRAME_DROP_ENABLED=true) — absent from tools/list when off, because per-table and per-canvas TTL already reclaim staged tables. Reach for it only to free a large table early in a long session.
• All three require CANVAS_PROVIDER_TYPE=duckdb; without it they return a canvas_disabled error and chembl_get_bioactivities degrades to a preview-only response.

Resources and prompts

Type	Name	Description
Resource	chembl://molecule/{chemblId}	A molecule record by ChEMBL ID — the same shape a chembl_search_molecules row carries (ID, names, structures, properties, max clinical phase).
Resource	chembl://target/{chemblId}	A target record by ChEMBL target ID — preferred name, type, organism, and component UniProt accessions + gene symbols.

All resource data is also reachable via the tools, so tool-only MCP clients lose nothing — the resources are convenience injectable-context mirrors of the per-record fetch. {chemblId} is validated against the CHEMBL\d+ pattern. 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.

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool and resource definitions — single file per primitive, framework handles registration and validation
• Unified error handling — handlers throw, framework catches, classifies, and formats
• Typed error contracts with recovery hints (missing_filter, missing_input, canvas_disabled)
• Pluggable auth (none, jwt, oauth) and swappable storage backends
• Structured logging with optional OpenTelemetry tracing
• STDIO and Streamable HTTP transports

ChEMBL-specific:

• Single keyless upstream client for the ChEMBL REST data API — Django-style filtered URL builder, page_meta pagination, withRetry-wrapped fetch + parse
• String → number | null numeric coercion at the service boundary (a missing potency becomes null, never 0 — the scientific-data fidelity rule)
• Bidirectional bioactivity: one tool serves both compound→target and target→compound, ranked on pchembl_value
• Structure search (exact / similarity / substructure) consolidated under one discovery tool via a search_type enum
• DataCanvas spill on the flagship: tens-of-thousands-of-row activity sets stream to a DuckDB table queryable via chembl_dataframe_query
• Server-level instructions carry the cross-server chain guidance and the ChEMBL CC BY-SA 3.0 attribution

Agent-friendly output:

• Provenance on every response — total-found counts, applied-filter echo, and a spill notice so agents know whether the preview is the full set or a slice of a canvas table
• Truncation disclosure — capped search results report shown / cap / totalCount so a page is never mistaken for the complete set
• Typed, recoverable errors — missing_filter / missing_input / canvas_disabled carry recovery hints, so callers correct the call without parsing prose
• Never fabricates — normalization and format() preserve null potency / units; a missing measurement renders as "not reported", never 0

Getting started

ChEMBL is keyless — no API key or account is required.

Add the following to your MCP client configuration file:

{
  "mcpServers": {
    "chembl-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/chembl-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "chembl-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/chembl-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "chembl-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/chembl-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

To unlock the analytical SQL path (the bioactivities spill and the chembl_dataframe_* tools), add "CANVAS_PROVIDER_TYPE": "duckdb" to the env.

Prerequisites

• Bun v1.3.0 or higher (or Node.js v24+).
• Optional: set CANVAS_PROVIDER_TYPE=duckdb to enable the DataCanvas SQL path for large bioactivity sets.

Installation

• Clone the repository:

git clone https://github.com/cyanheads/chembl-mcp-server.git

• Navigate into the directory:

cd chembl-mcp-server

• Install dependencies:

bun install

• Configure environment:

cp .env.example .env
# edit .env to override any defaults (all optional)

Configuration

All configuration is validated at startup via Zod schemas in src/config/server-config.ts. ChEMBL is keyless, so every variable is optional.

Variable	Description	Default
CANVAS_PROVIDER_TYPE	Set to duckdb to enable the bioactivity spill and the chembl_dataframe_* SQL tools. When none, large sets inline a preview but never spill.	none
CHEMBL_API_BASE_URL	Base URL for the ChEMBL REST data API. Override for a private mirror or pinned host.	https://www.ebi.ac.uk/chembl/api/data
CHEMBL_REQUEST_TIMEOUT_MS	Per-request timeout in milliseconds for upstream ChEMBL fetches.	30000
CHEMBL_MAX_PAGE_SIZE	ChEMBL per-page cap when streaming activity pages for the spill (max 1000).	1000
CHEMBL_DEFAULT_LIMIT	Default result limit applied when callers omit it.	25
CHEMBL_DATAFRAME_DROP_ENABLED	Register the opt-in chembl_dataframe_drop tool (absent from tools/list when off).	false
MCP_TRANSPORT_TYPE	Transport: stdio or http.	stdio
MCP_HTTP_PORT	Port for the HTTP server.	3010
MCP_AUTH_MODE	Auth mode: none, jwt, or oauth.	none
MCP_LOG_LEVEL	Log level (RFC 5424).	info
LOGS_DIR	Directory for log files (Node.js only).	<project-root>/logs
OTEL_ENABLED	Enable OpenTelemetry instrumentation.	false

See .env.example for the full list of optional overrides.

Running the server

Local development

• Build and run:

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:stdio
  # or
  bun run start:http
  

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security, changelog sync
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

docker build -t chembl-mcp-server .
docker run --rm -e MCP_TRANSPORT_TYPE=stdio chembl-mcp-server

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/chembl-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them. The fully-resolved @duckdb native binary is copied from the build stage so CANVAS_PROVIDER_TYPE=duckdb works at runtime.

Project structure

Directory	Purpose
src/index.ts	createApp() entry point — registers tools/resources and inits the ChEMBL service + optional canvas.
src/config	Server-specific environment variable parsing and validation with Zod.
src/mcp-server/tools/definitions	Tool definitions (*.tool.ts). Five ChEMBL tools plus the three chembl_dataframe_* canvas tools.
src/mcp-server/resources/definitions	Resource definitions (*.resource.ts). Molecule and target record mirrors.
src/services/chembl	The single ChEMBL upstream client — URL builder, pagination, numeric coercion, nested-structure flattening, activity page stream.
src/services/canvas-accessor.ts	Module-level holder for the optional DataCanvas wired in createApp({ setup }).
tests/	Unit and integration tests mirroring src/.

Development guide

See CLAUDE.md/AGENTS.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools and resources in the createApp() arrays
• Wrap the ChEMBL API: validate raw → normalize to the flat domain type → return the output schema; never fabricate missing fields (absent numerics become null, never 0)

Contributing

Issues and pull requests are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.