Research workbench
Design and synthesis of potent bace-1 inhibitors with cellular activity: structure-activity relationship of P1 substituents
Analyse Design and synthesis of potent bace-1 inhibitors with cellular activity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IVI
- Type
- protein
- Length
- 1,131 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
- 2LI, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 380 | 15% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- 2LI · N-[(1S,2R)-3-{[(5S)-5-(3-tert-butylphenyl)-4,5,6,7-tetrahydro-1H-indazol-5-yl]amino}-1-(3,5-difluorobenzyl)-2-hydroxypropyl]acetamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.76 | 0.78 | 113 | SO4, GOL, 2LI |
| 2 | 968 | 0.74 | 0.77 | 86 | SO4, GOL, 2LI |
| 3 | 413 | 0.65 | 0.79 | 43 | SO4, GOL, 2LI |
| 4 | 118 | 0.45 | 0.78 | 34 | empty |
| 5 | 65 | 0.29 | 0.74 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 608 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 570 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3IVI · Design and Synthesis of Potent BACE-1 Inhibitors with Cellular Activity… · 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 C against A, TM-score 0.99
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 3IVI · PDBe 3IVI · UniProt P56817
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