MolNFT v1 · #66631 · protein

Structure of bace (beta secretase) in complex with ligand EV2

3HW1 · Beta-secretase 1: “Structure of bace (beta secretase) in complex with ligand EV2”. X-ray diffraction, 1 ligand (EV2), 10 pockets (best druggability 0.75). MolNFT v1 #66631 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3HW1
Type: protein
Length: 1,116 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: EV2
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	370	15% helix, 41% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	371	13% helix, 42% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	375	15% helix, 41% strand	P56817

Ligands and binding sites

EV2 · 3-pyrrolidin-1-ylquinoxalin-2-amine · ligand · 3 copies · chains A, B, C
GOL · Glycerol · additive · chains C

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	575	0.75	0.82	71	EV2, GOL
2	513	0.63	0.76	41	EV2
3	80	0.60	0.89	30	empty
4	97	0.59	0.87	20	empty
5	211	0.59	0.80	36	EV2

Interfaces

2 interfaces between chains.

B–C · 834 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 613 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3HW1 · Structure of Bace (beta secretase) in complex with ligand EV2 · 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 3HW1 · PDBe 3HW1 · UniProt P56817

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