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Crystal structure of bace-1 in complex with inhibitor

Analyse Crystal structure of bace-1 in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CKP
Type: protein
Length: 1,132 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1
EC: 3.4.23.46
UniProt: P56817
Ligands: 012, CL
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	379	13% helix, 41% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	376	13% helix, 40% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	377	15% helix, 41% strand	P56817

Ligands and binding sites

012 · (4S)-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-1-(3-methoxybenzyl)-2-oxoimidazolidine-4-carboxamide · ligand · 3 copies · chains A, B, C
CL · Chloride ion · ion · 9 copies · chains A, C, 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	424	0.73	0.83	38	empty
2	572	0.71	0.80	65	012
3	492	0.69	0.79	56	012
4	414	0.64	0.78	39	012
5	162	0.54	0.80	35	empty

Interfaces

2 interfaces between chains.

B–C · 782 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 662 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3CKP · Crystal structure of BACE-1 in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · 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 P56817
Elsewhere: RCSB PDB 3CKP · PDBe 3CKP · UniProt P56817

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