Research workbench
Cathepsin-K in complex with miv-710
Analyse Cathepsin-K in complex with miv-710 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QLW
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin K
- EC
- 3.4.22.38
- UniProt
- P43235
- Ligands
- J5T, NA, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cathepsin K (EC 3.4.22.38) | protein | 216 | 28% helix, 22% strand | P43235 |
Ligands and binding sites
- J5T · ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.81 | 0.84 | 82 | empty |
| 2 | 509 | 0.72 | 0.82 | 62 | empty |
| 3 | 233 | 0.66 | 0.84 | 36 | empty |
| 4 | 75 | 0.52 | 0.85 | 24 | empty |
| 5 | 79 | 0.30 | 0.73 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 656 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 356 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 182 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 98 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 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 P43235
- Elsewhere: RCSB PDB 6QLW · PDBe 6QLW · UniProt P43235
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.