MolNFT v1 · #148787 · protein
Crystal structure of human bace-1 in complex with amino-1,4-oxazine compound 4
6FGY · Beta-secretase 1: “Crystal structure of human bace-1 in complex with amino-1,4-oxazine compound 4”. X-ray diffraction, 1 ligand (D9W), 3 pockets (best druggability 0.68). MolNFT v1 #148787 on GenesisL1: 3D structure, binding sites…
- PDB
- 6FGY
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- D9W
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 379 | 15% helix, 42% strand | P56817 |
Ligands and binding sites
- D9W · ~{N}-[3-[(3~{R})-5-azanyl-3-methyl-2,6-dihydro-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.68 | 0.78 | 54 | D9W |
| 2 | 135 | 0.47 | 0.78 | 32 | empty |
| 3 | 96 | 0.41 | 0.77 | 20 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6FGY · Crystal Structure of Human BACE-1 in Complex with amino-1,4-oxazine compound 4 · 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 0.98
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 6FGY · PDBe 6FGY · UniProt P56817
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