MolNFT v1 · #129320 · protein

Structure of cathepsin B1 from schistosoma mansoni in complex with WRR391 inhibitor

5OGQ · Cathepsin B-like peptidase (C01 family): “Structure of cathepsin B1 from schistosoma mansoni in complex with WRR391 inhibitor”. X-ray diffraction, 1 ligand (9U8), 8 pockets (best druggability 0.56). MolNFT v1 #129320 on GenesisL1…

PDB: 5OGQ
Type: protein
Length: 762 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin B-like peptidase (C01 family)
UniProt: Q8MNY2
Ligands: 9U8
Pockets: 8 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Cathepsin B-like peptidase (C01 family)	protein	254	28% helix, 21% strand	Q8MNY2

Ligands and binding sites

9U8 · ethyl 1-[[(2~{S})-3-(4-hydroxyphenyl)-1-oxidanylidene-1-[[(3~{S})-1-phenyl-5-pyridin-2-ylsulfonyl-pentan-3-yl]amino]propan-2-yl]carbamoyl]piperidine-4-carboxylate · ligand · 3 copies · chains A, B, C
ACT · Acetate ion · additive · chains B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.56	0.74	34	empty
2	204	0.52	0.77	25	empty
3	203	0.52	0.77	27	9U8
4	220	0.52	0.76	30	9U8
5	154	0.47	0.77	24	empty

Interfaces

2 interfaces between chains.

B–C · 386 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 78 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 18 disulfide, 3 covalent (disulfide, covalent ligand).

Compared structures

5OGQ · Structure of cathepsin B1 from Schistosoma mansoni in complex with WRR391 inhibitor · the same entry in another collection · chain A 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 Q8MNY2
Elsewhere: RCSB PDB 5OGQ · PDBe 5OGQ · UniProt Q8MNY2

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