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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: 5QBX
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: B8V
Pockets: 5 · best druggability 0.54

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cathepsin S (EC 3.4.22.27)	protein	219	29% helix, 24% strand	P25774

Ligands and binding sites

B8V · (2S)-1-[4-(2-methoxyphenyl)piperidin-1-yl]-3-{3-[3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl) phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propan-2-ol · ligand · 2 copies · chains A, B

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

Pockets

5 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	241	0.54	0.77	32	empty
2	89	0.45	0.80	19	empty
3	65	0.44	0.82	18	empty
4	107	0.41	0.76	23	empty
5	99	0.40	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 416 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5QBX · Crystal structure of human Cathepsin-S with bound ligand · 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 5QBX · PDBe 5QBX · UniProt P25774

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