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Crystal structure of the human BACE1 catalytic domain in complex with 4-(4-fluoro-benzyl)-piperazine-2-carboxylic ACID(3-mercapto-propyl)- amide

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

PDB: 2ZJK
Type: protein
Length: 1,111 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: F1K
Pockets: 12 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Beta-secretase 1 (EC 3.4.23.46)	protein	371	13% helix, 39% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	369	14% helix, 39% strand	P56817

Ligands and binding sites

F1K · (2S)-4-(4-fluorobenzyl)-N-(3-sulfanylpropyl)piperazine-2-carboxamide · ligand · 3 copies · chains A, B, C

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	413	0.65	0.78	41	F1K
2	395	0.64	0.78	40	F1K
3	345	0.63	0.79	48	F1K
4	66	0.61	0.91	27	empty
5	84	0.61	0.89	28	empty

Interfaces

2 interfaces between chains.

B–C · 673 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 181 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 3 covalent (disulfide, covalent ligand).

Compared structures

2ZJK · Crystal structure of the human BACE1 catalytic domain in complex with… · 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 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 P56817
Elsewhere: RCSB PDB 2ZJK · PDBe 2ZJK · UniProt P56817

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