MolNFT v1 · #140550 · protein
The crystal structure of lp-PLA2 in complex with a novel inhibitor
5YEA · Platelet-activating factor acetylhydrolase: “The crystal structure of lp-PLA2 in complex with a novel inhibitor”. X-ray diffraction, 2 ligands (8U9, SO4), 8 pockets (best druggability 0.61). MolNFT v1 #140550 on GenesisL1: 3D…
- PDB
- 5YEA
- Type
- protein
- Length
- 743 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
- 8U9, SO4
- Pockets
- 8 · best druggability 0.61
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 | 372 | 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
- 8U9 · 4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3-cyano-phenyl]sulfamoyl]benzoic acid · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.61 | 0.80 | 30 | 8U9 |
| 2 | 218 | 0.60 | 0.80 | 25 | 8U9 |
| 3 | 296 | 0.52 | 0.75 | 46 | empty |
| 4 | 116 | 0.45 | 0.78 | 20 | empty |
| 5 | 79 | 0.38 | 0.78 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5YEA · 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 5YEA · PDBe 5YEA · UniProt Q13093
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