MolNFT v1 · #67880 · protein

Potent beta-secretase 1 inhibitor

3IXK: “Potent beta-secretase 1 inhibitor”. X-ray diffraction, 1 ligand (929), 6 pockets (best druggability 0.73). MolNFT v1 #67880 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IXK
Type: protein
Length: 1,117 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: 929
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 1 (EC 3.4.23.46)	protein	373	14% helix, 42% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	371	16% helix, 40% strand	P56817

Ligands and binding sites

929 · N-[(2S,3S,5R)-1-[(3,5-difluorophenyl)methoxy]-3-hydroxy-5-methyl-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

6 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	482	0.73	0.82	62	929
2	457	0.72	0.82	55	929
3	392	0.69	0.81	50	929
4	257	0.49	0.74	40	empty
5	172	0.46	0.75	30	empty

Interfaces

2 interfaces between chains.

A–C · 421 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 405 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3IXK · Potent beta-secretase 1 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 3IXK · PDBe 3IXK · UniProt P56817

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