MolNFT v1 · #159067 · protein
Structure of bace-1 in complex with ligand 13
6OD6 · Beta-secretase 1: “Structure of bace-1 in complex with ligand 13”. X-ray diffraction, 1 ligand (M7D), 8 pockets (best druggability 0.72). MolNFT v1 #159067 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OD6
- Type
- protein
- Length
- 1,124 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
- M7D
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 14% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 14% helix, 39% strand | P56817 |
Ligands and binding sites
- M7D · N-{3-[(3R)-1-amino-3-methyl-3,4-dihydropyrrolo[1,2-a]pyrazin-3-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.72 | 0.78 | 82 | M7D |
| 2 | 599 | 0.70 | 0.79 | 65 | M7D |
| 3 | 526 | 0.67 | 0.78 | 56 | M7D |
| 4 | 165 | 0.61 | 0.83 | 26 | empty |
| 5 | 83 | 0.45 | 0.81 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 661 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 597 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 6OD6 · PDBe 6OD6 · UniProt P56817
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