MolNFT v1 · #131708 · protein
Crystal structure of human cathepsin-S with bound ligand
5QCH · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 2 ligands (BJS, SO4), 8 pockets (best druggability 0.59). MolNFT v1 #131708 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QCH
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin S
- EC
- 3.4.22.27
- UniProt
- P25774
- Ligands
- BJS, SO4
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cathepsin S (EC 3.4.22.27) | protein | 223 | 28% helix, 23% strand | P25774 |
| D | Cathepsin S (EC 3.4.22.27) | protein | 222 | 28% helix, 23% strand | P25774 |
Ligands and binding sites
- BJS · 2-(3-[3-({3-[(benzylamino)methyl]-4-chlorophenyl}ethynyl)-4-chlorophenyl]-1-{3-[(3S)-3-methylmorpholin-4-yl]propyl}-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl)-2-oxoacetamide · ligand · 4 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.59 | 0.76 | 46 | SO4, BJS |
| 2 | 51 | 0.56 | 0.90 | 23 | empty |
| 3 | 114 | 0.42 | 0.76 | 23 | empty |
| 4 | 124 | 0.42 | 0.76 | 25 | SO4 |
| 5 | 95 | 0.38 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- B–D · 623 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 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 5QCH · PDBe 5QCH · UniProt P25774
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