MolNFT v1 · #66820 · protein

Potent beta-secretase 1 hydroxyethylene inhibitor

3I25: “Potent beta-secretase 1 hydroxyethylene inhibitor”. X-ray diffraction, 1 ligand (MV7), 5 pockets (best druggability 0.75). MolNFT v1 #66820 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3I25
Type: protein
Length: 1,119 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: MV7
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Beta-secretase 1 (EC 3.4.23.46)	protein	373	15% helix, 42% strand	P56817

Ligands and binding sites

MV7 · N-[(2S,3S,5R)-1-(3,5-difluorophenoxy)-3-hydroxy-5-(2-methoxyethoxy)-6-[[(2S)-3-methyl-1-oxo-1-(phenylmethylamino)butan-2-yl]amino]-6-oxo-hexan-2-yl]-5-(methyl-methylsulfonyl-amino)-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide · ligand · 3 copies · chains A, B, C

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

Pockets

5 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	645	0.75	0.81	94	MV7
2	437	0.72	0.82	61	MV7
3	352	0.70	0.83	46	MV7
4	258	0.49	0.73	34	empty
5	72	0.28	0.73	19	empty

Interfaces

2 interfaces between chains.

A–C · 440 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3I25 · Potent Beta-Secretase 1 hydroxyethylene 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 3I25 · PDBe 3I25 · UniProt P56817

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