MolNFT v1 · #131733 · protein

Crystal structure of bace complex with BMC004

5QD6 · Beta-secretase 1: “Crystal structure of bace complex with BMC004”. X-ray diffraction, 1 ligand (E6S), 7 pockets (best druggability 0.80). MolNFT v1 #131733 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QD6
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: E6S
Pockets: 7 · best druggability 0.80

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

E6S · (3S,14R,16S)-16-[1,1-dihydroxy-2-({[3-(propan-2-yl) phenyl]methyl}amino)ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione · ligand · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.80	0.81	141	E6S
2	573	0.73	0.80	66	E6S
3	102	0.49	0.81	25	empty
4	112	0.43	0.77	31	empty
5	145	0.42	0.75	21	empty

Interfaces

2 interfaces between chains.

A–C · 1064 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 596 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QD6 · Crystal structure of BACE complex with BMC004 · 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 5QD6 · PDBe 5QD6 · UniProt P56817

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