MolNFT v1 · #74408 · protein

Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead

3OVX: “Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead”. X-ray diffraction, 1 ligand (O64), 2 pockets (best druggability 0.71). MolNFT v1 #74408 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OVX
Type: protein
Length: 434 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: O64
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cathepsin S (EC 3.4.22.27)	protein	217	31% helix, 23% strand	P25774

Ligands and binding sites

O64 · 2-chloro-N-[(1S)-1-formylpropyl]-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 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	489	0.71	0.81	61	O64
2	68	0.30	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 766 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3OVX · Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead · 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 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 P25774
Elsewhere: RCSB PDB 3OVX · PDBe 3OVX · UniProt P25774

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