MolNFT v1 · #49382 · protein
Structure of bace bound to SCH722924
2QMD · Beta-secretase 1: “Structure of bace bound to SCH722924”. X-ray diffraction, 1 ligand (CS7), 7 pockets (best druggability 0.67). MolNFT v1 #49382 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QMD
- 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
- CS7
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% 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, 39% strand | P56817 |
Ligands and binding sites
- CS7 · N'-[(1S,2R)-2-[(2R,4R)-4-(benzyloxy)pyrrolidin-2-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylisophthalamide · 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
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 | 361 | 0.67 | 0.81 | 46 | CS7 |
| 2 | 360 | 0.66 | 0.80 | 45 | CS7 |
| 3 | 75 | 0.57 | 0.88 | 27 | empty |
| 4 | 94 | 0.56 | 0.85 | 30 | empty |
| 5 | 169 | 0.52 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 232 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 2QMD · PDBe 2QMD · UniProt P56817
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