MolNFT v1 · #131688 · protein
Crystal structure of human cathepsin-S with bound ligand
5QBX · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (B8V), 5 pockets (best druggability 0.54). MolNFT v1 #131688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QBX
- 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
- B8V
- Pockets
- 5 · best druggability 0.54
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
- B8V · (2S)-1-[4-(2-methoxyphenyl)piperidin-1-yl]-3-{3-[3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl) phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propan-2-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.54 | 0.77 | 32 | empty |
| 2 | 89 | 0.45 | 0.80 | 19 | empty |
| 3 | 65 | 0.44 | 0.82 | 18 | empty |
| 4 | 107 | 0.41 | 0.76 | 23 | empty |
| 5 | 99 | 0.40 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 416 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 5QBX · PDBe 5QBX · UniProt P25774
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