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Crystal structure of human cathepsin-S with bound ligand

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

PDB: 5QCF
Type: protein
Length: 220 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin S
EC: 3.4.22.27
UniProt: P25774
Ligands: BJD, SO4
Pockets: 1 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin S (EC 3.4.22.27)	protein	220	29% helix, 24% strand	P25774

Ligands and binding sites

BJD · N-benzyl-1-{2-chloro-5-[(2-chloro-5-{5-(methylsulfonyl)-1-[3-(morpholin-4-yl)propyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}phenyl) ethynyl]phenyl}methanamine · ligand · chains A
SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.42	0.77	23	SO4

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

P25774 · AlphaFold monomer V2.0 prediction for cathepsin S (P25774) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 5QCF · PDBe 5QCF · UniProt P25774

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