MolNFT v1 · #131732 · protein

Crystal structure of bace complex with BMC009

5QD5 · Beta-secretase 1: “Crystal structure of bace complex with BMC009”. X-ray diffraction, 1 ligand (E6P), 9 pockets (best druggability 0.73). MolNFT v1 #131732 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QD5
Type: protein
Length: 1,132 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: E6P
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 16% 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	378	16% helix, 40% strand	P56817

Ligands and binding sites

E6P · (10S,12S)-17-chloro-12-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-10-methyl-7-oxa-2,13, 18-triazabicyclo[13.3.1]nonadeca-1(19),15,17-trien-14-one · ligand · 3 copies · chains A, B, C

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

Pockets

9 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	843	0.73	0.78	89	E6P
2	544	0.73	0.81	66	E6P
3	491	0.72	0.81	64	E6P
4	144	0.54	0.81	27	empty
5	106	0.47	0.80	25	empty

Interfaces

2 interfaces between chains.

A–C · 1096 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 561 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QD5 · Crystal structure of BACE complex with BMC009 · 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 5QD5 · PDBe 5QD5 · UniProt P56817

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