Research workbench
Crystal structure of human beta-secretase (bace) in the presence of an inhibitor (2)
Analyse Crystal structure of human beta-secretase (bace) in the presence of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HM1
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- LIQ
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 14% helix, 41% strand | P56817 |
Ligands and binding sites
- LIQ · N-{(1S)-2-({(1S,2R)-1-(3,5-difluorobenzyl)-3-[(3-ethylbenzyl)amino]-2-hydroxypropyl}amino)-2-oxo-1-[(pentylsulfonyl)methyl]ethyl}nicotinamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.66 | 0.78 | 43 | LIQ |
| 2 | 84 | 0.58 | 0.87 | 26 | empty |
Compared structures
- 2HM1 · Crystal Structure of human beta-secretase (BACE) in the presence of an inhibitor (2) · 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 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 2HM1 · PDBe 2HM1 · UniProt P56817
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