MolNFT v1 · #121382 · protein
BACE1 in complex with (R)-N-(3-(3-amino-2,5-dimethyl-1,1-dioxido-5,6- dihydro-2H-1,2,4-thiadiazin-5-yl)-4-fluorophenyl)-5- fluoropicolinamide
5HU1 · Beta-secretase 1: “BACE1 in complex with (R)-N-(3-(3-amino-2,5-dimethyl-1,1-dioxido-5,6…”. X-ray diffraction, 1 ligand (66F), 7 pockets (best druggability 0.67). MolNFT v1 #121382 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HU1
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 66F
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 388 | 16% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 386 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 66F · N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.67 | 0.80 | 45 | 66F |
| 2 | 386 | 0.66 | 0.79 | 41 | 66F |
| 3 | 75 | 0.58 | 0.88 | 25 | empty |
| 4 | 99 | 0.56 | 0.85 | 30 | empty |
| 5 | 123 | 0.51 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 243 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5HU1 · BACE1 in complex with (R)-N-(3-(3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thia… · 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 A against A, TM-score 1.00
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 5HU1 · PDBe 5HU1 · UniProt P56817
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