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Crystal structure of BACE1 with novel inhibitor

Analyse Crystal structure of BACE1 with novel inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FGX
Type: protein
Length: 380 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1; Inhibitor (2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-amino-3…
EC: 3.4.23.46
UniProt: P56817
Ligands: 2OP, URE, SO4
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	374	16% helix, 41% strand	P56817
B	Inhibitor (2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-amino-3- oxopropyl)-2,13-dibenzyl-12,22-dihydroxy-8-isobutyl-19-isopropyl-3,5, 17-trimethyl-4,7,10,15,18,21-hexaoxo-3,6,9,14,17,20-hexaazatricosan- 1-oic acid	protein	6	0% helix, 33% strand	—

Ligands and binding sites

2OP · (2S)-2-hydroxypropanoic acid · ligand · chains A, B
URE · Urea · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.35	0.74	21	2OP, URE

Interfaces

1 interface between chains.

A–B · 709 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 3 modified, 1 covalent (disulfide, nonstandard, covalent ligand).

Compared structures

4FGX · Crystal structure of bace1 with novel 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 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 P56817
Elsewhere: RCSB PDB 4FGX · PDBe 4FGX · UniProt P56817

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