MolNFT v1 · #126324 · protein
Fragment-based inhibitors of lipoprotein associated phospholipase A2
5LZ9 · Platelet-activating factor acetylhydrolase: “Fragment-based inhibitors of lipoprotein associated phospholipase A2”. X-ray diffraction, 3 ligands (7BR, NA, CL), 2 pockets (best druggability 0.58). MolNFT v1 #126324 on GenesisL1: 3D…
- PDB
- 5LZ9
- Type
- protein
- Length
- 370 residues
- Chains
- 1
- 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
- 7BR, NA, CL
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 370 | 35% helix, 21% strand | Q13093 |
Ligands and binding sites
- 7BR · 2-fluoranyl-5-[2-[(4~{S})-4-[4-methyl-1,1-bis(oxidanylidene)thian-4-yl]-2-oxidanylidene-pyrrolidin-1-yl]ethoxy]benzenecarbonitrile · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.58 | 0.78 | 29 | 7BR |
| 2 | 69 | 0.31 | 0.74 | 18 | empty |
Compared structures
- 5LZ9 · Fragment-based inhibitors of Lipoprotein associated Phospholipase A2 · 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 A 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 5LZ9 · PDBe 5LZ9 · UniProt Q13093
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