MolNFT v1 · #169326 · protein

Caspase-8 in complex with aomk inhibitor, ac-DW3-ke, forms tetrahedral adduct

6X8H: “Caspase-8 in complex with aomk inhibitor, ac-DW3-ke, forms tetrahedral adduct”. X-ray diffraction, 2 ligands (ACE, Y1Y), 2 pockets (best druggability 0.40). MolNFT v1 #169326 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6X8H
Type: protein
Length: 245 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-8; Ac-DW3-ke
EC: 3.4.22.61
UniProt: Q14790
Ligands: ACE, Y1Y
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-8 (EC 3.4.22.61)	protein	152	30% helix, 23% strand	Q14790
B	Caspase-8 (EC 3.4.22.61)	protein	89	33% helix, 20% strand	Q14790
C	Ac-DW3-ke	protein	4	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, C
Y1Y · 3-amino-2,3-dideoxy-5-O-(5-methylthiophene-2-carbonyl)-D-erythro-pentonic acid · ligand · chains A, B, C

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	123	0.40	0.75	20	ACE, Y1Y
2	57	0.34	0.77	13	empty

Interfaces

3 interfaces between chains.

A–B · 2257 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 274 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 188 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

6X8H · Caspase-8 in complex with AOMK inhibitor, Ac-DW3-KE, forms tetrahedral adduct · 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 B 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 6X8H · PDBe 6X8H · UniProt Q14790

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