Research workbench
Human bace-1 in complex with 6-ethyl-1-methyl-N-((1S)-2-oxo-1- (phenylmethyl)-3-(tetrahydro-2H-pyran-4-YLAMINO)PROPYL)-1,3,4,6- TETRAHYDRO(1,2)THIAZEPINO(5,4,3-CD)INDOLE-8-carboxamide 2,2-dioxide
Analyse Human bace-1 in complex with 6-ethyl-1-methyl-N-((1S)-2-oxo-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WF4
- Type
- protein
- Length
- 372 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
- ZY4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 372 | 15% helix, 42% strand | P56817 |
Ligands and binding sites
- ZY4 · N-[(1S)-1-benzyl-2,2-dihydroxy-3-(tetrahydro-2H-pyran-4-ylamino)propyl]-6-ethyl-1-methyl-1,3,4,6-tetrahydro[1,2]thiazepino[5,4,3-cd]indole-8-carboxamide 2,2-dioxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.69 | 0.82 | 50 | ZY4 |
| 2 | 132 | 0.47 | 0.78 | 26 | empty |
| 3 | 80 | 0.37 | 0.77 | 18 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2WF4 · Human BACE-1 in complex with 6-ethyl-1-methyl-N-((1S)-2-oxo-1-(phenylmethyl)-3-(tetrahydro… · 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 0.98
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 2WF4 · PDBe 2WF4 · UniProt P56817
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