Research workbench
Cathepsin L with a nitrile inhibitor
Analyse Cathepsin L with a nitrile inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJ8
- Type
- protein
- Length
- 219 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L1
- EC
- 3.4.22.15
- UniProt
- P07711
- Ligands
- YJ8
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin L1 (EC 3.4.22.15) | protein | 219 | 28% helix, 23% strand | P07711 |
Ligands and binding sites
- YJ8 · (2S,4R)-4-(2-chlorophenyl)sulfonyl-N-[1-(iminomethyl)cyclopropyl]-1-[1-(4-iodophenyl)cyclopropyl]carbonyl-pyrrolidine-2-carboxamide · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.32 | 0.76 | 18 | YJ8 |
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07711
- Elsewhere: RCSB PDB 2YJ8 · PDBe 2YJ8 · UniProt P07711
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