MolNFT v1 · #68747 · protein

Human bace-1 complex with nb-216

3K5C · Beta-secretase 1: “Human bace-1 complex with nb-216”. X-ray diffraction, 1 ligand (0BI), 8 pockets (best druggability 0.73). MolNFT v1 #68747 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K5C
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: 0BI
Pockets: 8 · 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	16% helix, 41% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	381	16% helix, 39% strand	P56817

Ligands and binding sites

0BI · (4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl) phenyl]cyclopropyl}amino)ethyl]-19-(methoxymethyl)-11-oxa-3,16-diazatric yclo[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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	671	0.73	0.80	78	0BI
2	591	0.72	0.80	74	0BI
3	646	0.71	0.79	68	0BI
4	66	0.57	0.89	18	empty
5	156	0.44	0.76	22	empty

Interfaces

2 interfaces between chains.

A–C · 1075 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 563 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3K5C · Human BACE-1 complex with NB-216 · 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 3K5C · PDBe 3K5C · UniProt P56817

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