MolNFT v1 · #28696 · protein
Crystal structure of human beta secretase complexed with nvp-AUR200
1YM2 · Beta-secretase 1: “Crystal structure of human beta secretase complexed with nvp-AUR200”. X-ray diffraction, 3 ligands (ACE, 24O, LYT), 11 pockets (best druggability 0.69). MolNFT v1 #28696 on GenesisL1: 3D structure, binding sites…
- PDB
- 1YM2
- Type
- protein
- Length
- 1,138 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; Nvp-AUR200 inhibitor
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- ACE, 24O, LYT
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 376 | 16% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 16% helix, 40% strand | P56817 |
| X, Y, Z | Nvp-AUR200 inhibitor | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, X, B, Y, C, Z
- 24O · (1R,2R)-2-[(1S,2S)-2-amino-1-hydroxy-4-methylpentyl]-4-oxocyclopentanecarboxylic acid · ligand · 3 copies · chains A, X, B, Y, C, Z
- LYT · Butylamine · ligand · 3 copies · chains A, B, X, Y, C, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.69 | 0.77 | 66 | 24O, LYT |
| 2 | 86 | 0.65 | 0.91 | 25 | 24O |
| 3 | 329 | 0.61 | 0.79 | 46 | empty |
| 4 | 140 | 0.60 | 0.84 | 36 | ACE, 24O |
| 5 | 98 | 0.57 | 0.85 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1014 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 10 hydrogen bonds · protein-protein
- B–Y · 485 Ų buried · 5 hydrogen bonds · protein-protein
- A–X · 463 Ų buried · 5 hydrogen bonds · protein-protein
- C–Z · 456 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 9 disulfide (covalent ligand, 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 1YM2 · PDBe 1YM2 · UniProt P56817
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