MolNFT v1 · #60121 · protein
Structure of bace bound to SCH726222
3CID · Beta-secretase 1: “Structure of bace bound to SCH726222”. X-ray diffraction, 1 ligand (318), 6 pockets (best druggability 0.68). MolNFT v1 #60121 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CID
- 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
- 318
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 15% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 15% helix, 39% strand | P56817 |
Ligands and binding sites
- 318 · N'-[(1S,2S)-2-[(4S)-1-benzyl-5-oxoimidazolidin-4-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide · ligand · 2 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · 3 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.68 | 0.81 | 44 | 318 |
| 2 | 344 | 0.65 | 0.80 | 45 | 318 |
| 3 | 79 | 0.59 | 0.88 | 26 | empty |
| 4 | 239 | 0.57 | 0.79 | 31 | empty |
| 5 | 85 | 0.52 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 251 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 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 3CID · PDBe 3CID · UniProt P56817
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