MolNFT v1 · #131739 · protein
Crystal structure of bace complex with BMC019 hydrolyzed
5QDC · Beta-secretase 1: “Crystal structure of bace complex with BMC019 hydrolyzed”. X-ray diffraction, 1 ligand (E77), 8 pockets (best druggability 0.77). MolNFT v1 #131739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QDC
- Type
- protein
- Length
- 1,112 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
- E77
- Pockets
- 8 · best druggability 0.77
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 | 367 | 16% helix, 42% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 15% helix, 42% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- E77 · (4S)-4-[(1R)-1,2-dihydroxyethyl]-N,N-dimethyl-2-oxo-11, 16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21), 6(22),7,9,17,19-hexaene-19-carboxamide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 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 | 1171 | 0.77 | 0.79 | 138 | GOL, E77 |
| 2 | 309 | 0.66 | 0.81 | 44 | GOL, E77 |
| 3 | 73 | 0.56 | 0.88 | 17 | empty |
| 4 | 198 | 0.50 | 0.76 | 44 | empty |
| 5 | 159 | 0.44 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1049 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 542 Ų buried · 8 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 5QDC · PDBe 5QDC · UniProt P56817
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