MolNFT v1 · #131685 · protein
Crystal structure of human cathepsin-S with bound ligand
5QBU · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (B8J), 4 pockets (best druggability 0.75). MolNFT v1 #131685 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QBU
- 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
- B8J
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 219 | 30% helix, 23% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 220 | 30% helix, 23% strand | P25774 |
Ligands and binding sites
- B8J · 1-[1-(3-{5-(1H-imidazole-5-carbonyl)-3-[4-(trifluoromethyl)phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propyl)piperidin-4-yl]-3-methyl-1,3-dihydro-2H-benzimidazol-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.75 | 0.81 | 71 | empty |
| 2 | 158 | 0.57 | 0.82 | 34 | empty |
| 3 | 146 | 0.46 | 0.77 | 29 | empty |
| 4 | 135 | 0.45 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 7 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 A 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 5QBU · PDBe 5QBU · UniProt P25774
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