MolNFT v1 · #68751 · protein

Human bace-1 complex with BJC060

3K5G · Beta-secretase 1: “Human bace-1 complex with BJC060”. X-ray diffraction, 1 ligand (BJC), 7 pockets (best druggability 0.74). MolNFT v1 #68751 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K5G
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: BJC
Pockets: 7 · 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, 40% strand	P56817

Ligands and binding sites

BJC · (1R,3S)-N-[(1S,2R)-1-benzyl-2-hydroxy-3-{[3-(1-methylethyl)benzyl]amino}propyl]-3-[1-methyl-1-(2-oxopiperidin-1-yl)ethy l]cyclohexanecarboxamide · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1125	0.74	0.77	115	BJC
2	553	0.71	0.80	66	BJC
3	450	0.69	0.80	45	BJC
4	145	0.55	0.82	30	empty
5	124	0.45	0.78	29	empty

Interfaces

2 interfaces between chains.

A–C · 1059 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 591 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3K5G · Human bace-1 complex with bjc060 · 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 3K5G · PDBe 3K5G · UniProt P56817

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