MolNFT v1 · #116842 · protein
Co-crystal of BACE1 with compound 0211
5DQC · Beta-secretase 1: “Co-crystal of BACE1 with compound 0211”. X-ray diffraction, 1 ligand (5E7), 8 pockets (best druggability 0.75). MolNFT v1 #116842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DQC
- Type
- protein
- Length
- 1,114 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
- 5E7
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 372 | 15% helix, 42% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 369 | 15% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 5E7 · N-[(2S,3R)-3-hydroxy-4-({(2S,3S)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.75 | 0.80 | 94 | 5E7 |
| 2 | 669 | 0.74 | 0.80 | 82 | 5E7 |
| 3 | 358 | 0.70 | 0.83 | 50 | 5E7 |
| 4 | 82 | 0.43 | 0.80 | 17 | empty |
| 5 | 89 | 0.34 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 445 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 402 Ų buried · 4 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 5DQC · PDBe 5DQC · UniProt P56817
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