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Structure of BACE1 complex with a syn-hea-type inhibitor

Analyse Structure of BACE1 complex with a syn-hea-type inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TRW
Type: protein
Length: 1,177 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1; L-alpha-glutamyl-L-isoleucyl-N-[(2R,3S)-1-{[(1S)-1…
EC: 3.4.23.46
UniProt: P56817
Ligands: LHE
Pockets: 16 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 1 (EC 3.4.23.46)	protein	389	16% helix, 39% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	390	14% helix, 38% strand	P56817
D, E, F	L-alpha-glutamyl-L-isoleucyl-N-[(2R,3S)-1-{[(1S)-1- CARBOXYBUTYL]AMINO}-2-hydroxy-5-methylhexan-3-yl]-3-thiophen-2-yl-L- alaninamide	protein	3	0% helix, 0% strand	—

Ligands and binding sites

LHE · N-[(2R,3S)-3-amino-2-hydroxy-5-methylhexyl]-L-norvaline · ligand · 3 copies · chains A, D, B, E, C, F

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

Pockets

16 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	171	0.67	0.87	36	LHE
2	173	0.65	0.85	35	LHE
3	213	0.64	0.83	40	empty
4	170	0.63	0.84	32	LHE
5	272	0.60	0.79	33	empty

Interfaces

6 interfaces between chains.

A–B · 1019 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 444 Å² buried · 1 hydrogen bond · protein-protein
B–C · 400 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 399 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 396 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 3 covalent, 3 modified (disulfide, covalent ligand, nonstandard).

Compared structures

4TRW · Structure of BACE1 complex with a syn-HEA-type inhibitor · the same entry in another collection · chain F against F, 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 4TRW · PDBe 4TRW · UniProt P56817

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