Research workbench
Crystal structure of LP_PLA2 in complex with novel inhibitor
Analyse Crystal structure of LP_PLA2 in complex with novel inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I8P
- Type
- protein
- Length
- 735 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
- VQ7
- Pockets
- 10 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 369 | 38% helix, 21% strand | Q13093 |
| B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 366 | 35% helix, 20% strand | Q13093 |
Ligands and binding sites
- VQ7 · 6-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]-4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3,5-bis(fluoranyl)phenyl]methoxy]-1-methyl-pyrimidin-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.58 | 0.80 | 24 | VQ7 |
| 2 | 206 | 0.55 | 0.78 | 32 | VQ7 |
| 3 | 296 | 0.52 | 0.74 | 44 | empty |
| 4 | 115 | 0.47 | 0.80 | 17 | empty |
| 5 | 90 | 0.40 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5I8P · Crystal structure of LP_PLA2 in complex with 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 5I8P · PDBe 5I8P · UniProt Q13093
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