Protein-Ligand Interaction Clusters

Clusters of similar binding sites in the PDB and analysis of various type of interactions within the clusters.

Database Query

Select the checkbox below depending upon the type of query you want to perform against the database. Queries can be combined by selecting multiple checkboxes (PLEASE NOTE: Some of the checkboxes may be disabled logically when multiple queries are combined). If you are unsure about the exact protein or ligand name, use 'Any text' field to find close matches.

Mouse over the text field to get information about each of them with examples.

If you find the database useful, Please cite: PLIC: protein-ligand interaction clusters. Database (Oxford). 2014 Apr 23;2014(0):bau029.


  • No. of Proteins : 30956
  • No. of Ligands : 11042
  • No. of Protein-Ligand Interactions : 84846
  • SCOP Classification
    Alpha and beta proteins (a/b): 6321
    Alpha and beta proteins (a+b): 3679
    All beta proteins: 3654
    All alpha proteins: 3007
    Multi-domain proteins: 442
    Membrane and cell surface proteins: 287
    Small proteins: 273
    Others: 110
  • No. of CATH superfamilies : 799
  • No. of unique EC numbers : 1553
  • No. of Binding Site Clusters : 10858
  • Enzyme Class Distribution
    Transferases: 7336
    Hydrolases: 6609
    Oxidoreductases: 5349
    Lyases: 1490
    Isomerases: 840
    Ligases: 693

Other Inhouse Databases and Servers

Latest Updates

Binding Site Residue number Rectification
Problem of having same residue numbers for different residues in binding site was rectified.
Jun 13, 2013
Selection of relevant ligands and binding sites
464844 binding sites extracted, but only the biologicall relevant ones - 84846 were chosen.
Mar 31, 2013
Protein Ligand Complexes
57002 protein-ligand complexes downloaded from PDB.
Jan 16, 2013