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Binary complex of native hache with donepezil

Analyse Binary complex of native hache with donepezil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O4W
Type: protein
Length: 1,080 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholinesterase
EC: 3.1.1.7
UniProt: P22303
Ligands: E20, NO3
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Acetylcholinesterase (EC 3.1.1.7)	protein	540	37% helix, 18% strand	P22303

Ligands and binding sites

E20 · 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl) methyl]piperidine · ligand · 2 copies · chains A, B
NO3 · Nitrate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	989	0.83	0.84	98	GOL, E20
2	400	0.62	0.77	35	empty
3	373	0.60	0.76	35	empty
4	83	0.43	0.80	19	GOL
5	112	0.43	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 640 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6O4W · Binary complex of native hAChE with Donepezil · the same entry in another collection · chain A against A, TM-score 1.00
P22303 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P22303) · a predicted model of the same protein · 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 P22303
Elsewhere: RCSB PDB 6O4W · PDBe 6O4W · UniProt P22303

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