MolNFT v1 · #161678 · protein

Cathepsin-K in complex with miv-710

6QLW · Cathepsin K: “Cathepsin-K in complex with miv-710”. X-ray diffraction, 3 ligands (J5T, NA, CL), 5 pockets (best druggability 0.81). MolNFT v1 #161678 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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.

Pocket	Volume (Å³)	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 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 356 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 303 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 182 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 98 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

6QLW · Cathepsin-K in complex with MIV-710 · the same entry in another collection · chain D against D, 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 1.00

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

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