Published 2025 | Version v2
Dataset Open

Lipid-Interacting LigAnd Complexes Database (LILAC-DB)

Authors/Creators

  • 1. ROR icon Scripps Research Institute

Description

Lipid-Interacting LigAnd Complexes Database (LILAC-DB) is a high quality dataset of PDB complexes of ligands binding at the protein-lipid bilayer Interface. LILAC-DB contains 231 unique small molecules interacting with 175 proteins, providing a diverse representation of ligand-protein-lipid interactions. 
All structures in this dataset are oriented by Orientations of Proteins in Membranes (OPM, https://opm.phar.umich.edu/) or Positioning of Proteins in Membranes (PPM, https://opm.phar.umich.edu/ppm_server) so that the plane representing the center of the bilayer is at Z=0. Below is a description of the contents of each file in the dataset.


There are two versions of this dataset:

1. LILAC-DB Refined (LILAC_DB_Refined)
This version includes every system that we identified as having a ligand bound at the protein-lipid interface, including multiple structures of the same protein-ligand complexes.

2. LILAC-DB Non-Redundant (LILAC_DB_Non_Redundant)
This version includes only one copy of a given ligand bound to a specific protein, determined by the protein's UniProt ID. The selection criteria are as follows:

In cases where there were multiple structures of the same protein-ligand pair, the highest resolution structure was kept.
If a structure had multiple copies of the same ligand bound, the ligand poses were clustered with a 2 Å cutoff, and only the first ligand in each cluster was retained. This step ensures that distinct binding poses are preserved, while only one copy of redundant poses (e.g., multimeric proteins with ligands bound in the same pose to each monomer) is kept.

The directory LILAC_DB/ contains two subdirectories:


LILAC_DB/
│
├── LILAC_DB_Refined/
│   ├── LILAC_DB_Refined.csv
│   ├── <pdb_id>/
│   │   ├── <ligand_id>/
│   │   │   ├── <ligand_id>_<ligand_copy>.pdb
│   │   │   ├── <ligand_id>_<ligand_copy>.sdf
│   │   │   ├── <ligand_id>_<ligand_copy>.csv
│   │   ├── <pdb_id>.pdb
│   │   ├── <pdb_id>_just_protein.pdb
│
├── LILAC_DB_Non_Redundant/
│   ├── LILAC_DB_Non_Redundant.csv
│   ├── <pdb_id>/
│   │   ├── <ligand_id>/
│   │   │   ├── <ligand_id>_<ligand_copy>.pdb
│   │   │   ├── <ligand_id>_<ligand_copy>.sdf
│   │   │   ├── <ligand_id>_<ligand_copy>.csv
│   │   ├── <pdb_id>.pdb
│   │   ├── <pdb_id>_just_protein.pdb
│
└── README.md

File Descriptions:
1. LILAC_DB_Refined.csv
This CSV file contains data for all systems of ligands bound at the protein-bilayer interface. It includes the following columns:

pdb_id: Protein Data Bank (PDB) identifier of the membrane protein.
ligand_id: Unique identifier for the ligand assigned by RCSB.
ligand_copy: The specific copy of the ligand.
Ligand SMILES: SMILES representation of the ligand.
1/2 Lipid Tail Thickness: Measurement of the lipid tail thickness of the bilayer from OPM/PPM.
Protein Name: Name of the protein (e.g., receptor or enzyme).
UniProt Accessions: UniProt database accession number for the protein(s).
Protein Classifications: Classification of the protein (s).
Organism: The organism from which the protein is derived.
Membrane: Which membrane(s) the protein is localized in.
2. LILAC_DB_Non_Redundant.csv
This CSV file contains data for unique protein-ligand pairs from the dataset. It includes the same columns as the "all" version but with only one ligand copy per protein, based on the criteria described above.

3. <pdb_id>.pdb
This file contains the 3D structure of the membrane protein in PDB format, oriented by OPM/PPM so that the plane representing the center of the bilayer is at Z=0.

4. <pdb_id>_just_protein.pdb
This file contains only the protein structure, oriented by OPM/PPM so that the plane representing the center of the bilayer is at Z=0, excluding any ligands, water molecules, or other heteroatoms.

5. <ligand_id>_<ligand_copy>.pdb
This file contains the 3D structure of a ligand in PDB format.

6. <ligand_id>_<ligand_copy>.sdf
This file contains the ligand structure in SDF format.

7. <ligand_id>_<ligand_copy>.csv
This CSV file contains a description of which atoms are exposed to the lipid bilayer. The file includes the following columns:

atom_idx: Index of the atom in the ligand.
element: Chemical element of the atom.
x_coord, y_coord, z_coord: Coordinates of the atom in 3D space.
touches_bilayer: Whether the atom is in contact with the lipid bilayer (True/False).

Files

LILAC_DB.zip

Files (394.8 MB)

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Additional details

Funding

National Institutes of Health
R01GM069832 GM069832

Dates

Created
2024-12-18