MolNFT v1 · #136681 · protein
BACE1 in complex with inhibitor 5G
5V0N · Beta-secretase 1: “BACE1 in complex with inhibitor 5G”. X-ray diffraction, 3 ligands (8W4, URE, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #136681 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V0N
- Type
- protein
- Length
- 1,121 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
- 8W4, URE, SO4
- Pockets
- 6 · best druggability 0.78
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 | 371 | 15% helix, 43% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 15% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- 8W4 · N-{(1S,2S)-1-[(2S)-4-benzyl-3-oxopiperazin-2-yl]-1-hydroxy-3-phenylpropan-2-yl}-7-ethyl-1,3,3-trimethyl-2,2-dioxo-1,2,3,4-tetrahydro-2lambda~6~-[1,2, 5]thiadiazepino[3,4,5-hi]indole-9-carboxamide · ligand · 3 copies · chains A, B, C
- URE · Urea · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.78 | 0.80 | 132 | 8W4 |
| 2 | 323 | 0.70 | 0.84 | 42 | SO4 |
| 3 | 360 | 0.66 | 0.80 | 42 | 8W4 |
| 4 | 324 | 0.65 | 0.81 | 39 | 8W4 |
| 5 | 66 | 0.28 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 709 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 5 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 5V0N · PDBe 5V0N · UniProt P56817
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