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
- 5QC5
- Type
- protein
- Length
- 440 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
- BAJ
- Pockets
- 4 · best druggability 0.75
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 | 220 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- BAJ · 1-[5-{1-[3-(4-tert-butylpiperidin-1-yl)propyl]-5-(methylsulfonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}-2-(trifluoromethyl)phenyl]-N-[(4-fluorophenyl)methyl]methanamine · 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 | 601 | 0.75 | 0.82 | 63 | empty |
| 2 | 83 | 0.50 | 0.83 | 21 | empty |
| 3 | 134 | 0.46 | 0.77 | 26 | empty |
| 4 | 142 | 0.44 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 6 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 5QC5 · PDBe 5QC5 · UniProt P25774
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