Research workbench
Structure of cathepsin K in complex with the azadipeptide nitrile inhibitor GU1303
Analyse Structure of cathepsin K in complex with the azadipeptide nitrile inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QBN
- Type
- protein
- Length
- 217 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin K
- EC
- 3.4.22.38
- UniProt
- P43235
- Ligands
- 9ZG, CL
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin K (EC 3.4.22.38) | protein | 217 | 26% helix, 24% strand | P43235 |
Ligands and binding sites
- 9ZG · (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl) amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate · ligand · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.35 | 0.77 | 17 | CL |
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7QBN · Structure of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303 · 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 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 P43235
- Elsewhere: RCSB PDB 7QBN · PDBe 7QBN · UniProt P43235
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