MolNFT v1 · #131700 · protein
Crystal structure of human cathepsin-S with bound ligand
5QC9 · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (BG7), 2 pockets (best druggability 0.45). MolNFT v1 #131700 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QC9
- 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
- BG7
- Pockets
- 2 · best druggability 0.45
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 | 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
- BG7 · N-{[5-{1-[3-(dimethylamino)propyl]-5-[(piperidin-4-yl) acetyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}-2-(trifluoromethyl)phenyl]methyl}-3-methylbut-2-enamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.45 | 0.76 | 25 | empty |
| 2 | 126 | 0.43 | 0.76 | 29 | BG7 |
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 5QC9 · PDBe 5QC9 · UniProt P25774
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