Datasets:

LiteFold
/

PDB-CCD

---
pretty_name: PDB Chemical Component Dictionary
license: other
tags:
- biology
- chemistry
- structural-biology
- pdb
- chemical-components
- mmcif
- parquet
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*.parquet
  - split: test
    path: data/test-*.parquet
---

# PDB Chemical Component Dictionary

PDB-CCD is the Chemical Component Dictionary used by the Protein Data Bank to describe residues, modified residues, ligands, solvents, and other chemical components in macromolecular structures.

## Splits

The split is deterministic by component identifier: `sha256(component_id) % 10`. Bucket `0` is `test`; buckets `1` through `9` are `train`.

| Split | Rows |
|---|---:|
| train | 45,045 |
| test | 5,009 |
| total | 50,054 |

## Dataset Statistics

| Field | Value |
|---|---:|
| Components | 50,054 |
| Released components | 49,292 |
| Obsolete components | 762 |
| Components with atoms | 49,947 |
| Components with bonds | 49,921 |
| Components with descriptors | 50,052 |
| Components with identifiers | 37,058 |
| Components with PCM annotations | 613 |
| Latest modified date in source | `2026-04-24` |

| Common component type | Rows |
|---|---:|
| NON-POLYMER | 26,117 |
| non-polymer | 19,493 |
| L-PEPTIDE LINKING | 923 |
| L-peptide linking | 580 |
| peptide-like | 556 |
| D-saccharide | 405 |
| DNA LINKING | 325 |
| RNA LINKING | 223 |

## Usage

Install the Hugging Face Datasets library:

```bash
pip install datasets
```

Load all splits:

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/PDB-CCD")
print(ds)

row = ds["train"][0]
print(row["component_id"], row["name"], row["formula"])
```

Load one split:

```python
from datasets import load_dataset

train = load_dataset("LiteFold/PDB-CCD", split="train")
test = load_dataset("LiteFold/PDB-CCD", split="test")
```

Stream rows without downloading the full table first:

```python
from datasets import load_dataset

stream = load_dataset("LiteFold/PDB-CCD", split="train", streaming=True)
for row in stream.take(5):
    print(row["component_id"], row["canonical_smiles"], row["atom_count"])
```

Filter released non-polymer components with InChIKeys:

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/PDB-CCD", split="train")
released = ds.filter(
    lambda row: row["release_status"] == "REL"
    and row["component_type"] in {"NON-POLYMER", "non-polymer"}
    and row["inchikey"] is not None
)
print(released[0])
```

Find components modified after a date:

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/PDB-CCD", split="train")
recent = ds.filter(lambda row: row["modified_date"] is not None and row["modified_date"] >= "2026-01-01")
print(recent[0]["component_id"], recent[0]["modified_date"])
```

## Columns

| Column | Description |
|---|---|
| `component_id` | Chemical component identifier. |
| `name` | Component name from `_chem_comp.name`. |
| `component_type` | Raw `_chem_comp.type` value. |
| `pdbx_type` | Raw `_chem_comp.pdbx_type` value. |
| `formula` | Chemical formula. |
| `formula_weight` | Formula weight as a float. |
| `formal_charge` | Formal charge as an integer. |
| `mon_nstd_parent_comp_id` | Parent component ID for non-standard monomers, when present. |
| `one_letter_code` | One-letter code, when present. |
| `three_letter_code` | Three-letter code, when present. |
| `pdbx_synonyms` | Synonym field from `_chem_comp`. |
| `synonym_names` | Synonyms from `pdbx_chem_comp_synonyms`. |
| `initial_date` | Initial component date. |
| `modified_date` | Last modified date. |
| `release_status` | Release status, such as `REL` or `OBS`. |
| `replaced_by` | Replacement component ID, when present. |
| `replaces` | Component ID replaced by this component, when present. |
| `atom_ids` | Atom identifiers from `chem_comp_atom`. |
| `atom_elements` | Element symbols for `atom_ids`. |
| `atom_charges` | Atom charges. |
| `atom_aromatic_flags` | Atom aromatic flags. |
| `atom_leaving_flags` | Atom leaving-atom flags. |
| `atom_stereo_configs` | Atom stereochemistry flags. |
| `atom_count` | Number of atoms. |
| `heavy_atom_count` | Number of non-hydrogen atoms. |
| `hydrogen_atom_count` | Number of hydrogen atoms. |
| `bond_atom_id_1` | First atom ID for each bond. |
| `bond_atom_id_2` | Second atom ID for each bond. |
| `bond_orders` | Bond order values. |
| `bond_aromatic_flags` | Bond aromatic flags. |
| `bond_stereo_configs` | Bond stereochemistry flags. |
| `bond_count` | Number of bonds. |
| `descriptor_types` | Descriptor types such as `SMILES`, `SMILES_CANONICAL`, `InChI`, and `InChIKey`. |
| `descriptors` | Descriptor values. |
| `canonical_smiles` | First `SMILES_CANONICAL` descriptor. |
| `smiles` | First `SMILES` descriptor. |
| `inchi` | First `InChI` descriptor. |
| `inchikey` | First `InChIKey` descriptor. |
| `identifier_types` | Identifier types from `pdbx_chem_comp_identifier`. |
| `identifiers` | Identifier values. |
| `systematic_names` | Identifier values whose type is `SYSTEMATIC NAME`. |
| `audit_actions` | Audit action types. |
| `audit_dates` | Audit dates. |
| `related_component_ids` | Related component IDs, when present. |
| `pcm_ids` | Protein modification annotation IDs, when present. |
| `pcm_modified_residue_ids` | Modified residue IDs from PCM annotations. |
| `feature_types` | Feature types from `pdbx_chem_comp_feature`. |
| `feature_values` | Feature values from `pdbx_chem_comp_feature`. |
| `split_bucket` | Deterministic split bucket from `sha256(component_id) % 10`. |

# Citation

```
@article{westbrook2015pdbccd,
  title   = {The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank},
  author  = {Westbrook, John D. and Shao, Chuming and Feng, Zukang and Zhuravleva, Maria and Velankar, Sameer and Young, Jasmine},
  journal = {Bioinformatics},
  volume  = {31},
  number  = {8},
  pages   = {1274--1278},
  year    = {2015},
  doi     = {10.1093/bioinformatics/btu789}
}
```