MolNFT v1 · #131726 · protein

Crystal structure of bace complex with BMC015

5QCZ · Beta-secretase 1: “Crystal structure of bace complex with BMC015”. X-ray diffraction, 1 ligand (E5V), 8 pockets (best druggability 0.76). MolNFT v1 #131726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QCZ
Type: protein
Length: 1,131 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: E5V
Pockets: 8 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Beta-secretase 1 (EC 3.4.23.46)	protein	377	15% helix, 42% strand	P56817

Ligands and binding sites

E5V · (4S)-4-{(S)-hydroxy[(3r,6r)-6-(methoxymethyl)morpholin-3-yl]methyl}-19-(methoxymethyl)-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9, 17,19-hexaen-2-one · ligand · 3 copies · chains A, B, C

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.76	0.82	92	E5V
2	422	0.71	0.82	57	E5V
3	558	0.70	0.79	63	E5V
4	83	0.61	0.89	26	empty
5	160	0.55	0.81	30	empty

Interfaces

2 interfaces between chains.

A–C · 1111 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 588 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QCZ · Crystal structure of BACE complex with BMC015 · 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 5QCZ · PDBe 5QCZ · UniProt P56817

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