MolNFT v1 · #131693 · protein
Crystal structure of human cathepsin-S with bound ligand
5QC2 · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 1 ligand (BQP), 4 pockets (best druggability 0.75). MolNFT v1 #131693 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QC2
- Type
- protein
- Length
- 438 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
- BQP
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin S (EC 3.4.22.27) | protein | 219 | 31% helix, 23% strand | P25774 |
Ligands and binding sites
- BQP · 2-[1-(cyclohexylmethyl)piperidin-4-yl]-1-{3-[3-{[2-(4-fluoropiperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-1-(3-hydroxypropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethan-1-one · 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 | 643 | 0.75 | 0.81 | 79 | empty |
| 2 | 117 | 0.51 | 0.81 | 26 | empty |
| 3 | 149 | 0.44 | 0.76 | 29 | empty |
| 4 | 114 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5QC2 · PDBe 5QC2 · UniProt P25774
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