ChEMBL Download
v1.0.0Fetch ChEMBL compound structure and metadata files by ChEMBL molecule ID.
Fetch ChEMBL compound structure and metadata files by ChEMBL molecule ID.
ProteinIQ retrieves a ChEMBL molecule by its CHEMBL identifier and returns the source JSON record and an SDF download link. Enter an ID such as CHEMBL25, choose JSON, SDF, or both, then download the selected files for compound registration, cheminformatics, or ligand preparation.
For aspirin, enter CHEMBL25 and keep Output format on All formats. The returned filenames are:
chembl-CHEMBL25-json.json
chembl-CHEMBL25-sdf.sdfChEMBL Download is an identifier-based retrieval tool for ChEMBL, EMBL-EBI's curated database of bioactive, drug-like molecules. It retrieves the molecule record and chemical structure for one known ChEMBL compound, rather than searching an assay collection or predicting a compound property.
ChEMBL combines curated chemistry with calculated molecular properties and links to bioactivity, target, assay, and drug-development information. A CHEMBL molecule identifier is the stable starting point when a compound has already been selected from a ChEMBL report, publication, dataset, or screening list. For example, CHEMBL25 identifies aspirin in the current database.
The downloaded record is useful for preserving an exact structure and its source identifier alongside a compound shortlist. It does not by itself establish experimental potency, target selectivity, or a docking-ready protonation state. Those questions depend on the associated assays and on the preparation required by the next workflow step.
| Input | Description |
|---|---|
Entry ID | A ChEMBL molecule ID in the form CHEMBL followed by digits, such as CHEMBL25, CHEMBL941, or CHEMBL1201585. The lookup is intended for a molecule ID, not a compound name, SMILES string, InChIKey, target ID, assay ID, or publication ID. |
ChEMBL IDs should be retained exactly as returned by the database. A preferred name can change as curation evolves, while the identifier is the practical key for tracing a compound record. When only a name or structure is known, find and confirm the intended molecule in ChEMBL first, especially where salts, stereoisomers, parent compounds, or related analogues are possible matches.
| Setting | Options | Effect |
|---|---|---|
Database | ChEMBL by default | Keeps the lookup on ChEMBL. Selecting another database changes to that database's retrieval workflow, which requires its own identifier type. |
Output format | All formats (default), JSON, SDF | All formats lists both ChEMBL file links. Selecting one format limits the result to that file type; availability depends on the molecule record. |
| File | Filename example | Contents and typical use |
|---|---|---|
| JSON | chembl-CHEMBL25-json.json | The ChEMBL molecule endpoint response. Use it to preserve structured source metadata and identifiers in a script, manifest, or analysis record. |
| SDF | chembl-CHEMBL25-sdf.sdf | An MDL Structure Data File for the molecule. Use it as a chemical-structure input for inspection, conversion, or a ligand-preparation workflow. |
The JSON record contains available molecule properties, including molecule type, molecular formula, molecular weight, calculated AlogP, and canonical SMILES. Missing values do not imply a zero value or an invalid compound.
The JSON file is the most useful archival output. It keeps the source response intact and can include the molecule_chembl_id, preferred name, molecular type, calculated properties, canonical SMILES, and InChIKey. The exact field set varies with the molecule and with ChEMBL curation, so downstream parsers should tolerate absent optional fields.
The SDF file is a structure exchange format, not a complete experimental report. It represents the selected molecule record and can be passed into tools that accept SDF, but it does not encode every ChEMBL assay, target relationship, publication, or clinical annotation. ChEMBL's molecule API offers compound-level information, while activities, assays, mechanisms, targets, and documents are separate resources.
An SDF structure should also not be treated as automatically ready for every modeling task. Protonation, tautomer choice, stereochemistry, conformer generation, partial charges, and atom typing can affect a docking calculation. Inspect the chemical form before using it as a ligand input. SDF to SMILES is useful for checking or extracting a line notation, while Open Babel can convert a confirmed SDF into another supported structure format.
ChEMBL Download fits after compound identity has been established and before a structure must be moved into a local analysis or modeling workflow.
CHEMBL ID, retrieval date, and JSON response alongside a hit list so the source record can be revisited after a ChEMBL release updates its annotations.For a record keyed by a PubChem CID, name, or InChIKey, PubChem Download is the appropriate retrieval route. BindingDB search is available for looking up reported protein-ligand affinity records.
ChEMBL Download retrieves one molecule record and its available JSON and SDF representations. It does not perform a keyword search, retrieve a batch of compound IDs, download a full ChEMBL release, or return a complete compound-plus-bioactivity SD file. It also does not standardize the structure for a particular force field, generate a three-dimensional conformer, calculate properties, or determine whether a compound is commercially available.
For release-specific or large-scale analysis, use the official ChEMBL database downloads and record the ChEMBL release version. The live API and the molecule data returned here reflect the current database release, so a later retrieval can contain revised properties, identifiers, or annotations.
Enter one identifier or compound name on a single line, up to 200 characters. Surrounding spaces are ignored. These lookups need an internet connection: ProteinIQ retrieves the record from the selected database, and file downloads contact its file service.
If a text file cannot be loaded in the browser, a warning appears and its download link stays available. A listed link does not guarantee that the database currently serves that file. Retry the download or check the original database record; a connection failure is different from an unknown entry.
No. This tool retrieves the molecule resource. Target, assay, and activity records are separate resources in the ChEMBL web services.
Not every ChEMBL molecule record has a downloadable chemical structure. This is particularly relevant for some biological therapeutics. Keep the JSON record and check its molecule_structures field and the ChEMBL compound page.
Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey.
Run Open Babel online with molecular format conversion, coordinate generation, and hydrogen options.
Extract canonical SMILES strings from SDF ligand files, one record at a time or in batch.
Generate 3D SDF files from SMILES strings with batch conversion and downloadable combined outputs.
Generate SMILES strings from InChI identifiers for search, filtering, and modeling workflows.
Extract canonical SMILES strings from MDL MOL ligand files for cheminformatics workflows.
Extract canonical SMILES strings from MOL2 ligand files for cheminformatics workflows.
Convert ligand and peptide PDB coordinates to SDF with RDKit bond perception.
Export ligand poses from Meeko-prepared PDBQT to SDF while recovering chemical connectivity.
Convert SDF ligands to PDBQT with Meeko, preserving supplied coordinates.