MolNFT v1 · #69937 · protein

Structure of bace bound to SCH723873

3L5D · Beta-secretase 1: “Structure of bace bound to SCH723873”. X-ray diffraction, 1 ligand (BDV), 7 pockets (best druggability 0.64). MolNFT v1 #69937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3L5D
Type: protein
Length: 775 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1
EC: 3.4.23.46
UniProt: P56817
Ligands: BDV
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	386	15% helix, 39% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	389	16% helix, 40% strand	P56817

Ligands and binding sites

BDV · 1-butyl-3-(4-{[(2Z,4R)-2-imino-4-methyl-4-(2-methylpropyl)-5-oxoimidazolidin-1-yl]methyl}benzyl)urea · ligand · 2 copies · chains A, B
TAR · D(-)-tartaric acid · additive · 3 copies · chains A, B

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

Pockets

7 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	497	0.64	0.76	40	BDV
2	77	0.58	0.88	28	empty
3	77	0.53	0.86	24	empty
4	246	0.51	0.75	35	BDV
5	156	0.49	0.78	24	empty

Interfaces

1 interface between chains.

A–B · 292 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3L5D · Structure of BACE Bound to SCH723873 · 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 1.00

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 3L5D · PDBe 3L5D · UniProt P56817

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