MolNFT v1 · #131692 · protein
Crystal structure of human cathepsin-S with bound ligand
5QC1 · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (B9S), 4 pockets (best druggability 0.75). MolNFT v1 #131692 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QC1
- Type
- protein
- Length
- 442 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
- B9S
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin S (EC 3.4.22.27) | protein | 221 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- B9S · (2S)-1-(4,4-dimethylpiperidin-1-yl)-3-{3-[3-({[(4-fluorophenyl)methyl]amino}methyl)-4-(trifluoromethyl) phenyl]-5-(methylsulfonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propan-2-ol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.75 | 0.81 | 75 | empty |
| 2 | 77 | 0.50 | 0.84 | 18 | empty |
| 3 | 117 | 0.43 | 0.77 | 25 | empty |
| 4 | 126 | 0.41 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 5 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 5QC1 · PDBe 5QC1 · UniProt P25774
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