MolNFT v1 · #89254 · protein
Structure of bace bound to 5-(3-(5-chloropyridin-3-YL)PHENYL)-5- cyclopropyl-2-imino-3-methylimidazolidin-4-one
4DJX · Beta-secretase 1: “Structure of bace bound to 5-(3-(5-chloropyridin-3-YL)PHENYL)-5…”. X-ray diffraction, 1 ligand (0KQ), 7 pockets (best druggability 0.69). MolNFT v1 #89254 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4DJX
- Type
- protein
- Length
- 779 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 0KQ
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 16% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 0KQ · (2E,5R)-5-[3-(5-chloropyridin-3-yl)phenyl]-5-cyclopropyl-2-imino-3-methylimidazolidin-4-one · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.69 | 0.80 | 43 | 0KQ |
| 2 | 538 | 0.67 | 0.78 | 45 | 0KQ |
| 3 | 69 | 0.57 | 0.89 | 28 | empty |
| 4 | 84 | 0.53 | 0.85 | 26 | empty |
| 5 | 117 | 0.51 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 275 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4DJX · Structure of BACE Bound to 5-(3-(5-chloropyridin-3-yl)phenyl)-5-cyclopropyl-2-imino-3-meth… · the same entry in another collection · chain A against A, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 4DJX · PDBe 4DJX · UniProt P56817
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