SMILES to PDB Converter
In short: Convert a SMILES string to a downloadable 3D PDB file. It is free, works in your web browser and needs no download.
Convert a SMILES string to a 3D PDB file using a public chemistry conversion endpoint. You can preview and download the generated PDB text.
Input and output formats
| Input: SMILES | Output: PDB | |
|---|---|---|
| Full name | SMILES (Simplified Molecular Input Line Entry System) | PDB (Protein Data Bank format) |
| What it holds | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. | 3D atom coordinates in fixed columns. Used for proteins and small molecules. |
| File or form | .smi or plain text | .pdb |
File Format Explained
SMILES is a compact text identifier for molecular connectivity. It is easy to paste and store, but it does not contain explicit 3D coordinates.
PDB stores atom coordinates in a structural biology format. PDB is useful for 3D visualization, molecular modeling, and workflows that expect coordinate files.
A SMILES to PDB conversion generates a coordinate draft from connectivity. Validate stereochemistry, protonation, and conformer geometry before using the PDB in docking or computational chemistry.
What you get and how to use it
The converter generates a 3D conformer from the SMILES connectivity and writes it as PDB, with one HETATM line per atom giving its x, y, z coordinates in ångströms. This is useful for viewing a small molecule in 3D software, preparing a ligand for modelling, or creating a quick 3D picture for teaching.
How to use it
- Paste a SMILES, for example caffeine
CN1C=NC2=C1C(=O)N(C(=O)N2C)C. - Convert and preview the PDB text.
- Download the .pdb file and open it in a molecular viewer.
Things to know
- One conformer: flexible molecules have many shapes. The file contains one reasonable geometry, not necessarily the bioactive or lowest-energy one.
- Stereochemistry: specify @/@@ for chiral centres and / or \ for double-bond geometry, otherwise the geometry may be chosen arbitrarily.
- Bond orders: the PDB format does not reliably store bond orders, so some programs re-infer them. If you need bond orders preserved, consider SMILES to MOL2 or SMILES to SDF.
For docking with AutoDock-family tools, use SMILES to PDBQT.
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