Research workbench

Caspase 8 with covalent inhibitor

Analyse Caspase 8 with covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KJQ
Type: protein
Length: 242 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-8
EC: 3.4.22.61
UniProt: Q14790
Ligands: B94
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-8 (EC 3.4.22.61)	protein	152	31% helix, 23% strand	Q14790
B	Caspase-8 (EC 3.4.22.61)	protein	90	32% helix, 20% strand	Q14790

Ligands and binding sites

B94 · (3S)-3-({[(5S,8R)-2-(3-carboxypropyl)-8-(2-{[(4-chlorophenyl)acetyl]amino}ethyl)-1,3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazin-5-yl]carbonyl}amino)-4-oxopentanoic acid · ligand · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.47	0.75	23	B94
2	53	0.38	0.80	12	B94

Interfaces

1 interface between chains.

A–B · 2279 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3KJQ · Caspase 8 with covalent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q14790 · AlphaFold monomer V2.0 prediction for caspase-8 (Q14790) · 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 Q14790
Elsewhere: RCSB PDB 3KJQ · PDBe 3KJQ · UniProt Q14790

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