MolNFT v1 · #141840 · protein
Crystal structure of the human platelet-activating factor receptor in complex with abt-491
5ZKQ · Platelet-activating factor RECEPTOR,ENDOLYSIN,ENDOLYSIN…: “Crystal structure of the human platelet-activating factor receptor in complex with abt-491”. X-ray diffraction, 3 ligands (9EU, ZN, SO4), 4 pockets (best druggability 0.79).…
- PDB
- 5ZKQ
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-activating factor RECEPTOR,ENDOLYSIN,ENDOLYSIN, platelet-activating factor…
- EC
- 3.2.1.17
- UniProt
- P25105, P00720
- Ligands
- 9EU, ZN, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor RECEPTOR,ENDOLYSIN,ENDOLYSIN, platelet-activating factor receptor (EC 3.2.1.17) | protein | 279 | 77% helix, 4% strand | P25105, P00720 |
| B | Platelet-activating factor RECEPTOR,ENDOLYSIN,ENDOLYSIN, platelet-activating factor receptor (EC 3.2.1.17) | protein | 399 | 73% helix, 3% strand | P25105, P00720 |
Ligands and binding sites
- 9EU · 4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.79 | 0.87 | 43 | 9EU, OLC |
| 2 | 1085 | 0.78 | 0.79 | 104 | 9EU, OLC |
| 3 | 189 | 0.49 | 0.75 | 22 | empty |
| 4 | 126 | 0.48 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 725 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZKQ · Crystal structure of the human platelet-activating factor receptor in complex with ABT-491 · the same entry in another collection · chain A against A, TM-score 1.00
- P25105 · AlphaFold monomer V2.0 prediction for platelet-activating factor receptor (P25105) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P25105
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 5ZKQ · PDBe 5ZKQ · UniProt P25105 · UniProt P00720
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.