MolNFT v1 · #106847 · protein
Structure of BACE1 complex with a hea-type inhibitor
4TRY · Beta-secretase 1: “Structure of BACE1 complex with a hea-type inhibitor”. X-ray diffraction, 1 ligand (36D), 15 pockets (best druggability 0.65). MolNFT v1 #106847 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TRY
- Type
- protein
- Length
- 1,172 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; Glu-ile-tih-thc-nva
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 36D
- Pockets
- 15 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 40% strand | P56817 |
| B, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 388 | 15% helix, 38% strand | P56817 |
| D, E, F | Glu-ile-tih-thc-nva | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 36D · N-[(2R,3S)-3-amino-2-hydroxy-4-(thiophen-2-yl) butanoyl]-L-norvaline · ligand · 3 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.65 | 0.86 | 31 | 36D |
| 2 | 54 | 0.64 | 0.94 | 15 | 36D |
| 3 | 286 | 0.63 | 0.80 | 43 | empty |
| 4 | 115 | 0.59 | 0.85 | 21 | 36D |
| 5 | 268 | 0.58 | 0.78 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1112 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 440 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 409 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 covalent, 3 modified (disulfide, covalent ligand, nonstandard).
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 4TRY · PDBe 4TRY · UniProt P56817
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