Research workbench
Exploitation of a novel binding pocket in human lipoprotein-associated phospholipase A2 (lp-PLA<SUB>2</SUB>) discovered through X-ray fragment screening
Analyse Exploitation of a novel binding pocket in human lipoprotein-associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JAL
- Type
- protein
- Length
- 371 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
- 6HO, MG, CL
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 36% 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 |
Ligands and binding sites
- 6HO · (2,5-dihydro-1H-pyrrol-1-yl)(3-fluorophenyl)methanone · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 225 | 0.58 | 0.79 | 27 | DMS, 6HO |
| 2 | 77 | 0.32 | 0.74 | 16 | empty |
Compared structures
- 5JAL · Exploitation of a Novel Binding Pocket in Human 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 5JAL · PDBe 5JAL · UniProt Q13093
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