MolNFT v1 · #120872 · protein
Bace-1 in complex with (7AR)-7A-(5-cyanothiophen-2-yl)-6-(5-fluoro-4- methyl-6-(METHYLTHIO)PYRIMIDIN-2-yl)-3-methyl-4-oxooctahydro-2H- PYRROLO[3,4-D]PYRIMIDIN-2-iminium
5HDZ · Beta-secretase 1: “Bace-1 in complex with (7AR)-7A-(5-cyanothiophen-2-yl)-6-(5-fluoro-4…”. X-ray diffraction, 1 ligand (954), 7 pockets (best druggability 0.65). MolNFT v1 #120872 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HDZ
- Type
- protein
- Length
- 773 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
- 954
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 386 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 954 · 5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylsulfanyl)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile · ligand · 2 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 | 446 | 0.65 | 0.78 | 37 | 954 |
| 2 | 412 | 0.64 | 0.78 | 39 | 954 |
| 3 | 73 | 0.56 | 0.87 | 24 | empty |
| 4 | 71 | 0.56 | 0.87 | 26 | empty |
| 5 | 83 | 0.55 | 0.86 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 283 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5HDZ · BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methyl-6-(methylthio)… · the same entry in another collection · chain B against B, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 5HDZ · PDBe 5HDZ · UniProt P56817
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