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
- 5QC4
- Type
- protein
- Length
- 441 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
- BC7
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 221 | 30% helix, 23% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 220 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- BC7 · 2-[5-[5-ethanoyl-1-[(2~{R})-2-oxidanyl-3-[4-(2-oxidanylpropan-2-yl)piperidin-1-yl]propyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]-2-(trifluoromethyl)phenyl]sulfanyl-1-pyrrolidin-1-yl-ethanone · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.75 | 0.81 | 77 | empty |
| 2 | 81 | 0.52 | 0.84 | 18 | empty |
| 3 | 175 | 0.51 | 0.78 | 31 | empty |
| 4 | 95 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 616 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 5QC4 · PDBe 5QC4 · UniProt P25774
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.