MolNFT v1 · #93688 · protein
Structure of bace bound to (S)-3-(5-(2-imino-1,4-dimethyl-6- oxohexahydropyrimidin-4-YL)THIOPHEN-3-YL)BENZONITRILE
4HA5 · Beta-secretase 1: “Structure of bace bound to (S)-3-(5-(2-imino-1,4-dimethyl-6…”. X-ray diffraction, 1 ligand (13W), 7 pockets (best druggability 0.64). MolNFT v1 #93688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4HA5
- Type
- protein
- Length
- 776 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
- 13W
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 15% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 386 | 16% helix, 38% strand | P56817 |
Ligands and binding sites
- 13W · 3-{5-[(2E,4S)-2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.64 | 0.77 | 42 | 13W |
| 2 | 69 | 0.62 | 0.91 | 29 | empty |
| 3 | 353 | 0.59 | 0.76 | 38 | 13W |
| 4 | 99 | 0.54 | 0.84 | 29 | empty |
| 5 | 151 | 0.50 | 0.78 | 30 | TLA |
Interfaces
1 interface between chains.
- A–B · 252 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4HA5 · Structure of BACE Bound to (S)-3-(5-(2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl)thi… · 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 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 4HA5 · PDBe 4HA5 · UniProt P56817
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.