MolNFT v1 · #131710 · protein
Crystal structure of human cathepsin-S with bound ligand
5QCJ · Cathepsin S: “Crystal structure of human cathepsin-S with bound ligand”. X-ray diffraction, 2 ligands (BJY, SO4), 4 pockets (best druggability 0.66). MolNFT v1 #131710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QCJ
- Type
- protein
- Length
- 660 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin S
- EC
- 3.4.22.27
- UniProt
- P25774
- Ligands
- BJY, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 221 | 27% helix, 24% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 220 | 29% helix, 24% strand | P25774 |
| C | Cathepsin S (EC 3.4.22.27) | protein | 219 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- BJY · 5-hydroxy-3-{1-[(2S)-2-hydroxy-3-{5-(methylsulfonyl)-3-[4-(trifluoromethyl)phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propyl]piperidin-4-yl}-1H-pyrrolo[3,2-c]pyridin-5-ium · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.66 | 0.77 | 63 | SO4 |
| 2 | 200 | 0.46 | 0.74 | 28 | empty |
| 3 | 104 | 0.40 | 0.76 | 21 | SO4 |
| 4 | 53 | 0.25 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 659 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 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 5QCJ · PDBe 5QCJ · UniProt P25774
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