MolNFT v1 · #89357 · protein

Cathepsin K inhibitor

4DMY: “Cathepsin K inhibitor”. X-ray diffraction, 2 ligands (0LC, SO4), 2 pockets (best druggability 0.47). MolNFT v1 #89357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DMY
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: 0LC, SO4
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cathepsin K (EC 3.4.22.38)	protein	215	28% helix, 23% strand	P43235

Ligands and binding sites

0LC · (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.47	0.75	23	empty
2	120	0.45	0.78	27	GOL

Interfaces

1 interface between chains.

A–B · 460 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

4DMY · Cathepsin K inhibitor · 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 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 4DMY · PDBe 4DMY · UniProt P43235

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.