MolNFT v1 · #131724 · protein

Crystal structure of bace complex with BMC007

5QCX · Beta-secretase 1: “Crystal structure of bace complex with BMC007”. X-ray diffraction, 1 ligand (E5D), 10 pockets (best druggability 0.74). MolNFT v1 #131724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QCX
Type: protein
Length: 1,135 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: E5D
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 1 (EC 3.4.23.46)	protein	377	15% helix, 41% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	381	15% helix, 39% strand	P56817

Ligands and binding sites

E5D · (9R,11S)-3-ethyl-11-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-9-methyl-3,12-diazabicyclo[12.3.1]octadeca-1(18),14,16-triene-2,13-dione · ligand · 3 copies · chains A, B, 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	653	0.74	0.81	79	E5D
2	514	0.73	0.81	66	E5D
3	366	0.69	0.82	47	E5D
4	123	0.53	0.82	22	empty
5	150	0.51	0.79	27	empty

Interfaces

2 interfaces between chains.

A–C · 1073 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 587 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QCX · Crystal structure of BACE complex with BMC007 · 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 5QCX · PDBe 5QCX · UniProt P56817

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