MolNFT v1 · #68748 · protein
Crystal structure of bace-1 in complex with AHM178
3K5D · Beta-secretase 1: “Crystal structure of bace-1 in complex with AHM178”. X-ray diffraction, 1 ligand (XLI), 9 pockets (best druggability 0.70). MolNFT v1 #68748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3K5D
- Type
- protein
- Length
- 1,126 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
- XLI
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 39% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 376 | 15% helix, 39% strand | P56817 |
Ligands and binding sites
- XLI · N-acetyl-L-leucyl-N-[(4S,5S,7R)-8-(butylamino)-5-hydroxy-2,7-dimethyl-8-oxooctan-4-yl]-L-methioninamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.70 | 0.77 | 83 | XLI |
| 2 | 380 | 0.66 | 0.80 | 40 | XLI |
| 3 | 358 | 0.66 | 0.80 | 37 | XLI |
| 4 | 168 | 0.62 | 0.84 | 41 | empty |
| 5 | 299 | 0.60 | 0.79 | 52 | empty |
Interfaces
2 interfaces between chains.
- A–B · 980 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
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 3K5D · PDBe 3K5D · UniProt P56817
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