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Crystal structure of human cathepsin S bound to a non-covalent inhibitor

Analyse Crystal structure of human cathepsin S bound to a non-covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P6E
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin S
EC: 3.4.22.27
UniProt: P25774
Ligands: 2FC, SO4
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cathepsin S (EC 3.4.22.27)	protein	219	29% helix, 23% strand	P25774

Ligands and binding sites

2FC · N-[(8R)-8-(benzoylamino)-5,6,7,8-tetrahydronaphthalen-2-yl]-4-methylpiperazine-1-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.70	0.80	59	2FC
2	86	0.33	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 775 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4P6E · Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · 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 P25774
Elsewhere: RCSB PDB 4P6E · PDBe 4P6E · UniProt P25774

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