Research workbench
Crystal structure of cathepsin K complexed with 7-methyl- substituted azepan-3-one compound
Analyse Crystal structure of cathepsin K complexed with 7-methyl- substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FTD
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin K
- EC
- 3.4.22.38
- UniProt
- P61277
- Ligands
- ILI
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin K (EC 3.4.22.38) | protein | 215 | 29% helix, 22% strand | P61277 |
Ligands and binding sites
- ILI · N-[(1S)-1-({[(3S,4S,7R)-3-hydroxy-7-methyl-1-(pyridin-2-ylsulfonyl)-2,3,4,7-tetrahydro-1H-azepin-4-yl]amino}carbonyl)-3-methylbutyl]-1-benzofuran-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.59 | 0.92 | 21 | empty |
| 2 | 194 | 0.53 | 0.78 | 34 | empty |
| 3 | 179 | 0.49 | 0.77 | 23 | empty |
| 4 | 130 | 0.43 | 0.76 | 26 | empty |
| 5 | 53 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2FTD · Crystal structure of Cathepsin K complexed with 7-Methyl-Substituted Azepan-3-one compound · the same entry in another collection · chain A against A, TM-score 1.00
- P61277 · AlphaFold monomer V2.0 prediction for cathepsin K (P61277) · 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 P61277
- Elsewhere: RCSB PDB 2FTD · PDBe 2FTD · UniProt P61277
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