MolNFT v1 · #123134 · protein
Exploitation of a novel binding pocket in human lipoprotein-associated phospholipase A2 (lp-PLA<SUB>2</SUB>) discovered through X-ray fragment screening
5JAO · Platelet-activating factor acetylhydrolase: “Exploitation of a novel binding pocket in human lipoprotein-associated phospholipase A2 (lp-PLA<SUB>2</SUB>)…”. X-ray diffraction, 3 ligands (6HX, CA, CL), 2 pockets (best druggability…
- PDB
- 5JAO
- 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
- 6HX, CA, 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
- 6HX · 2'-chloro-6-methyl[1,1'-biphenyl]-3-amine · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 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 | 240 | 0.58 | 0.78 | 36 | CL, DMS, 6HX |
| 2 | 80 | 0.34 | 0.74 | 18 | empty |
Compared structures
- 5JAO · 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 5JAO · PDBe 5JAO · UniProt Q13093
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.