MolNFT v1 · #38736 · protein
Crystal structure of cathepsin S in complex with a nonpeptidic inhibitor.
2H7J: “Crystal structure of cathepsin S in complex with a nonpeptidic inhibitor.”. X-ray diffraction, 2 ligands (H7J, P15), 2 pockets (best druggability 0.69). MolNFT v1 #38736 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H7J
- Type
- protein
- Length
- 435 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
- H7J, P15
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 218 | 29% helix, 23% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 217 | 29% helix, 24% strand | P25774 |
Ligands and binding sites
- H7J · N-[(1S)-1-{1-[(1R,3E)-1-acetylpent-3-en-1-yl]-1H-1,2,3-triazol-4-yl}-1,2-dimethylpropyl]benzamide · ligand · 2 copies · chains A, B
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.69 | 0.80 | 54 | H7J, P15 |
| 2 | 66 | 0.29 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 779 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
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 2H7J · PDBe 2H7J · UniProt P25774
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