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
- 5QC0
- 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
- BQJ
- Pockets
- 5 · 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
- BQJ · 2-(dimethylamino)-1-[4-(2-oxo-2-{3-[3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-1-propyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethyl)piperidin-1-yl]ethan-1-one · 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 | 517 | 0.75 | 0.83 | 54 | empty |
| 2 | 100 | 0.49 | 0.81 | 25 | empty |
| 3 | 146 | 0.44 | 0.76 | 28 | BQJ |
| 4 | 115 | 0.40 | 0.75 | 21 | BQJ |
| 5 | 53 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 595 Ų buried · 7 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 5QC0 · PDBe 5QC0 · UniProt P25774
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