MolNFT v1 · #80999 · protein

Crystal structure of bace with compound 12

3UDP · Beta-secretase 1: “Crystal structure of bace with compound 12”. X-ray diffraction, 2 ligands (09D, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #80999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3UDP
Type: protein
Length: 394 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: 09D, ZN
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	394	15% helix, 39% strand	P56817

Ligands and binding sites

09D · (4S)-6-bromo-3,4-dihydro-2H-thiochromen-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

3 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	490	0.72	0.81	60	09D, PEG
2	59	0.30	0.75	15	empty
3	51	0.23	0.72	15	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3UDP · Crystal Structure of BACE with Compound 12 · 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 0.96

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 3UDP · PDBe 3UDP · UniProt P56817

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.