Research workbench
Crystal structure of human cathepsin-S with bound ligand
Analyse Crystal structure of human cathepsin-S with bound ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QBY
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin S
- EC
- 3.4.22.27
- UniProt
- P25774
- Ligands
- N2A
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin S (EC 3.4.22.27) | protein | 219 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- N2A · N-[2-chloro-5-(1-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-6-oxo-1,6-dihydropyrimidin-5-yl)benzyl]-4-fluorobenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.41 | 0.77 | 20 | empty |
| 2 | 103 | 0.39 | 0.76 | 19 | empty |
| 3 | 53 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 185 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P25774
- Elsewhere: RCSB PDB 5QBY · PDBe 5QBY · UniProt P25774
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