MolNFT v1 · #140549 · protein
The crystal structure of lp-PLA2 in complex with a novel inhibitor
5YE9 · Platelet-activating factor acetylhydrolase: “The crystal structure of lp-PLA2 in complex with a novel inhibitor”. X-ray diffraction, 2 ligands (8U6, SO4), 7 pockets (best druggability 0.59). MolNFT v1 #140549 on GenesisL1: 3D…
- PDB
- 5YE9
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-activating factor acetylhydrolase
- EC
- 3.1.1.47
- UniProt
- Q13093
- Ligands
- 8U6, SO4
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 369 | 37% helix, 20% strand | Q13093 |
| B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 371 | 37% helix, 20% strand | Q13093 |
Ligands and binding sites
- 8U6 · N-[4-[(3-cyano-4-naphthalen-2-yloxy-phenyl) sulfamoyl]phenyl]ethanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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 | 221 | 0.59 | 0.79 | 26 | 8U6 |
| 2 | 204 | 0.59 | 0.80 | 28 | 8U6 |
| 3 | 227 | 0.56 | 0.79 | 28 | SO4 |
| 4 | 362 | 0.56 | 0.75 | 48 | empty |
| 5 | 90 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5YE9 · The crystal structure of Lp-PLA2 in complex with a novel inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q13093 · AlphaFold monomer V2.0 prediction for platelet-activating factor acetylhydrolase (Q13093) · 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 Q13093
- Elsewhere: RCSB PDB 5YE9 · PDBe 5YE9 · UniProt Q13093
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.