MolNFT v1 · #67238 · protein
Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements
3IEJ: “Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements”. X-ray diffraction, 1 ligand (599), 4 pockets (best druggability 0.75). MolNFT v1 #67238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IEJ
- 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
- 599
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin S (EC 3.4.22.27) | protein | 221 | 30% helix, 23% strand | P25774 |
| B | Cathepsin S (EC 3.4.22.27) | protein | 221 | 30% helix, 23% strand | P25774 |
Ligands and binding sites
- 599 · 2-[3-{4-chloro-3-[(4-chlorophenyl)ethynyl]phenyl}-1-(3-morpholin-4-ylpropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]-2-oxoethanol · 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 | 639 | 0.75 | 0.82 | 85 | empty |
| 2 | 100 | 0.51 | 0.82 | 21 | empty |
| 3 | 124 | 0.45 | 0.78 | 28 | 599 |
| 4 | 140 | 0.44 | 0.76 | 27 | 599 |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3IEJ · Pyrazole-based Cathepsin S Inhibitors with Arylalkynes as P1 Binding Elements · the same entry in another collection · chain A against A, TM-score 1.00
- P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 3IEJ · PDBe 3IEJ · UniProt P25774
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.