MolNFT v1 · #93470 · protein
Structure of bace bound to 3-(5-((7AR)-2-imino-6-(6-methoxypyridin-2- yl)-3-methyl-4-oxooctahydro-1H-PYRROLO[3,4-D]PYRIMIDIN-7A-yl) thiophen-3-YL)BENZONITRILE
4H3F · Beta-secretase 1: “Structure of bace bound to 3-(5-((7AR)-2-imino-6-(6-methoxypyridin-2…”. X-ray diffraction, 1 ligand (10O), 7 pockets (best druggability 0.71). MolNFT v1 #93470 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4H3F
- 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
- 10O
- Pockets
- 7 · best druggability 0.71
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 | 15% helix, 39% strand | P56817 |
Ligands and binding sites
- 10O · 3-{5-[(2E,4aR,7aR)-2-imino-6-(6-methoxypyridin-2-yl)-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile · ligand · 2 copies · chains A, B
- TLA · L(+)-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 | 502 | 0.71 | 0.80 | 46 | 10O |
| 2 | 449 | 0.65 | 0.78 | 41 | 10O |
| 3 | 82 | 0.57 | 0.87 | 30 | empty |
| 4 | 89 | 0.53 | 0.84 | 28 | empty |
| 5 | 94 | 0.52 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 268 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4H3F · Structure of BACE Bound to 3-(5-((7aR)-2-imino-6-(6-methoxypyridin-2-yl)-3-methyl-4-oxooct… · 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 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 4H3F · PDBe 4H3F · UniProt P56817
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