MolNFT v1 · #15989 · protein
Crystal structure of the cysteine protease human cathepsin K in complex with a covalent azepanone inhibitor
1NLJ: “Crystal structure of the cysteine protease human cathepsin K in complex with a covalent azepanone inhibitor”. X-ray diffraction, 1 ligand (2CA), 3 pockets (best druggability 0.40). MolNFT v1 #15989 on GenesisL1: 3D structure…
- PDB
- 1NLJ
- 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
- P43235
- Ligands
- 2CA
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin K (EC 3.4.22.38) | protein | 215 | 29% helix, 21% strand | P43235 |
Ligands and binding sites
- 2CA · Benzofuran-2-carboxylic acid {(S)-3-methyl-1-[3-oxo-1-(pyridin-2-ylsulfonyl)azepan-4-ylcarbamoyl]butyl}amide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.40 | 0.75 | 28 | 2CA |
| 2 | 89 | 0.33 | 0.73 | 22 | empty |
| 3 | 67 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 406 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1NLJ · Crystal structure of the cysteine protease human cathepsin K in complex with a covalent… · the same entry in another collection · chain A against A, TM-score 1.00
- P43235 · AlphaFold monomer V2.0 prediction for cathepsin K (P43235) · a predicted model of the same protein · chain B 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 P43235
- Elsewhere: RCSB PDB 1NLJ · PDBe 1NLJ · UniProt P43235
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