MolNFT v1 · #54132 · protein

Human bace-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)- 1-methyl-2-OXOETHYL)AMINO)-2-hydroxy-1-(PHENYLMETHYL)PROPYL)-3- (ethylamino)-5-(2-oxo-1-PYRROLIDINYL)BENZAMIDE

2XFJ · Beta-secretase 1: “Human bace-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)…”. X-ray diffraction, 1 ligand (VG5), 2 pockets (best druggability 0.72). MolNFT v1 #54132 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2XFJ
Type: protein
Length: 373 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1
EC: 3.4.23.46
UniProt: P56817
Ligands: VG5
Pockets: 2 · best druggability 0.72

Structure

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

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

Ligands and binding sites

VG5 · N-[(1S,2R)-1-benzyl-3-{[(1S)-2-(cyclohexylamino)-1-methyl-2-oxoethyl]amino}-2-hydroxypropyl]-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl)benzamide · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	453	0.72	0.82	63	VG5
2	125	0.47	0.79	27	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2XFJ · Human BACE-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)… · 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 0.98

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 2XFJ · PDBe 2XFJ · UniProt P56817

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