MolNFT v1 · #106848 · protein

Structure of BACE1 complex with 2-thiophenyl hea-type inhibitor

4TRZ · Beta-secretase 1: “Structure of BACE1 complex with 2-thiophenyl hea-type inhibitor”. X-ray diffraction, 1 ligand (TVA), 10 pockets (best druggability 0.79). MolNFT v1 #106848 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4TRZ
Type: protein
Length: 1,173 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1; 2-thiophenyl hea-type inhibitor
EC: 3.4.23.46
UniProt: P56817
Ligands: TVA
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Beta-secretase 1 (EC 3.4.23.46)	protein	388	15% helix, 39% strand	P56817
D, E, F	2-thiophenyl hea-type inhibitor	protein	3	0% helix, 0% strand	—

Ligands and binding sites

TVA · N-[(2R,3S)-3-amino-2-hydroxy-4-(thiophen-2-yl)butyl]-L-norvaline · ligand · 3 copies · chains A, D, B, E, C, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	785	0.79	0.82	88	TVA
2	326	0.68	0.82	66	empty
3	276	0.64	0.81	45	empty
4	145	0.63	0.85	34	empty
5	132	0.55	0.82	20	TVA

Interfaces

5 interfaces between chains.

A–B · 1042 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 567 Å² buried · 4 hydrogen bonds · protein-protein
C–F · 412 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 390 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 388 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 covalent, 3 modified (disulfide, covalent ligand, nonstandard).

Compared structures

4TRZ · Structure of BACE1 complex with 2-thiophenyl HEA-type inhibitor · the same entry in another collection · chain F against F, TM-score 1.00
P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain C 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 4TRZ · PDBe 4TRZ · UniProt P56817

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