MolNFT v1 · #131686 · protein
Crystal structure of human cathepsin-S with bound ligand
5QBV · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (N2D), 3 pockets (best druggability 0.43). MolNFT v1 #131686 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QBV
- Type
- protein
- Length
- 439 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
- N2D
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 220 | 29% helix, 24% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 219 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- N2D · 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-dihydropyridazin-3-yl)benzyl]benzamide · 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 | 135 | 0.43 | 0.76 | 25 | empty |
| 2 | 128 | 0.42 | 0.76 | 25 | empty |
| 3 | 74 | 0.30 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 238 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
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 P25774
- Elsewhere: RCSB PDB 5QBV · PDBe 5QBV · UniProt P25774
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