MolNFT v1 · #68750 · protein

Human bace-1 complex with AYH011

3K5F · Beta-secretase 1: “Human bace-1 complex with AYH011”. X-ray diffraction, 1 ligand (AYH), 6 pockets (best druggability 0.73). MolNFT v1 #68750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K5F
Type: protein
Length: 1,127 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: AYH
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	373	15% helix, 41% strand	P56817
B, C	Beta-secretase 1 (EC 3.4.23.46)	protein	377	16% helix, 41% strand	P56817

Ligands and binding sites

AYH · (1R,3S)-3-[1-(acetylamino)-1-methylethyl]-N-[(1S,2S,4R)-1-benzyl-5-(butylamino)-2-hydroxy-4-methyl-5-oxopentyl]cyclohexanecarboxamide · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.73	0.79	83	AYH
2	584	0.72	0.80	66	AYH
3	408	0.70	0.81	50	AYH
4	208	0.56	0.79	25	empty
5	112	0.47	0.79	25	empty

Interfaces

2 interfaces between chains.

A–C · 486 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 476 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3K5F · Human BACE-1 COMPLEX WITH AYH011 · 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 3K5F · PDBe 3K5F · UniProt P56817

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