MolNFT v1 · #131701 · protein
Crystal structure of human cathepsin-S with bound ligand
5QCA · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 2 ligands (BGJ, SO4), 4 pockets (best druggability 0.49). MolNFT v1 #131701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QCA
- Type
- protein
- Length
- 437 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
- BGJ, SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 219 | 27% helix, 24% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 218 | 27% helix, 24% strand | P25774 |
Ligands and binding sites
- BGJ · 1-{4-[(2-chloro-5-{1-[3-(4-cyclopropylpiperazin-1-yl) propyl]-5-(methylsulfonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}phenyl)ethynyl]phenyl}-N-[(4-chlorophenyl)methyl]methanamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.49 | 0.82 | 22 | empty |
| 2 | 99 | 0.41 | 0.78 | 25 | SO4 |
| 3 | 88 | 0.39 | 0.77 | 19 | empty |
| 4 | 51 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1018 Ų buried · 14 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 5QCA · PDBe 5QCA · UniProt P25774
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