Research workbench
Crystal structure of LP_PLA2 in complex with darapladib
Analyse Crystal structure of LP_PLA2 in complex with darapladib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I9I
- Type
- protein
- Length
- 734 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
- 5HV, SO4
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 371 | 36% helix, 21% strand | Q13093 |
| B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 363 | 37% helix, 21% strand | Q13093 |
Ligands and binding sites
- 5HV · N-[2-(diethylamino)ethyl]-2-{2-[(4-fluorobenzyl)sulfanyl]-4-oxo-4,5,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin-1-yl}-N-{[ 4'-(trifluoromethyl)biphenyl-4-yl]methyl}acetamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.57 | 0.79 | 27 | 5HV |
| 2 | 199 | 0.56 | 0.79 | 27 | 5HV |
| 3 | 281 | 0.51 | 0.75 | 41 | empty |
| 4 | 122 | 0.49 | 0.80 | 17 | empty |
| 5 | 95 | 0.38 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5I9I · Crystal structure of LP_PLA2 in complex with Darapladib · 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 5I9I · PDBe 5I9I · UniProt Q13093
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