MolNFT v1 · #87105 · protein

Mouse cathepsin S with covalent ligand

4BQV: “Mouse cathepsin S with covalent ligand”. X-ray diffraction, 1 ligand (8PW), 15 pockets (best druggability 0.86). MolNFT v1 #87105 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BQV
Type: protein
Length: 1,752 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin S
EC: 3.4.22.27
UniProt: O70370
Ligands: 8PW
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cathepsin S (EC 3.4.22.27)	protein	219	27% helix, 23% strand	O70370

Ligands and binding sites

8PW · (2S,4R)-N-(1-cyanocyclopropyl)-1-(1-methylcyclopropanecarbonyl)-4-[4-(2,2,2-trifluoroethoxy)-2-(trifluoromethyl)phenyl]sulfonylpyrrolidine-2-carboxamide · ligand · 8 copies · chains A, F, B, E, C, D, G, H

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1065	0.86	0.87	126	8PW
2	942	0.77	0.79	85	8PW
3	689	0.69	0.77	81	empty
4	203	0.61	0.82	47	8PW
5	194	0.60	0.82	33	8PW

Interfaces

13 interfaces between chains.

A–D · 674 Å² buried · 4 hydrogen bonds · protein-protein
E–G · 670 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 643 Å² buried · 2 hydrogen bonds · protein-protein
F–H · 632 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 409 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 8 covalent (disulfide, covalent ligand).

Compared structures

4BQV · Mouse cathepsin S with covalent ligand · the same entry in another collection · chain H against H, TM-score 1.00
O70370 · AlphaFold monomer V2.0 prediction for cathepsin S (O70370) · a predicted model of the same protein · chain C 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 O70370
Elsewhere: RCSB PDB 4BQV · PDBe 4BQV · UniProt O70370

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