MolNFT v1 · #97295 · protein

Bace-1 inhibitor complex

4K9H · Beta-secretase 1: “Bace-1 inhibitor complex”. X-ray diffraction, 1 ligand (1QU), 12 pockets (best druggability 0.69). MolNFT v1 #97295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4K9H
Type: protein
Length: 1,109 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: 1QU
Pockets: 12 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Beta-secretase 1 (EC 3.4.23.46)	protein	370	16% helix, 41% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	369	15% helix, 40% strand	P56817

Ligands and binding sites

1QU · 1-cyclopentyl-N-[(2S,3R)-3-hydroxy-1-phenyl-4-{[3-(trifluoromethyl)benzyl]amino}butan-2-yl]-6-oxo-5-(2-oxopyrrolidin-1-yl)-1,6-dihydropyridine-3-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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	356	0.69	0.82	45	1QU
2	339	0.68	0.82	40	1QU
3	338	0.68	0.82	51	1QU
4	317	0.59	0.77	44	empty
5	266	0.58	0.78	35	empty

Interfaces

3 interfaces between chains.

B–C · 1082 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 467 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 370 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

4K9H · Bace-1 inhibitor complex · 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 4K9H · PDBe 4K9H · UniProt P56817

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