MolNFT v1 · #109820 · protein
Idelalisib bound to the P110 subunit of PI3K delta
4XE0 · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Idelalisib bound to the P110 subunit of PI3K delta”. X-ray diffraction, 1 ligand (40L), 13 pockets (best druggability 0.82). MolNFT v1 #109820 on GenesisL1: 3D structure…
- PDB
- 4XE0
- Type
- protein
- Length
- 815 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
- EC
- 2.7.1.153
- UniProt
- O35904
- Ligands
- 40L
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) | protein | 815 | 46% helix, 18% strand | O35904 |
Ligands and binding sites
- 40L · 5-fluoro-3-phenyl-2-[(1S)-1-(7H-purin-6-ylamino)propyl]quinazolin-4(3H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.82 | 0.83 | 80 | empty |
| 2 | 598 | 0.68 | 0.78 | 66 | empty |
| 3 | 300 | 0.68 | 0.83 | 40 | empty |
| 4 | 120 | 0.65 | 0.88 | 24 | empty |
| 5 | 236 | 0.64 | 0.82 | 30 | 40L |
Compared structures
- 4XE0 · Idelalisib bound to the p110 subunit of PI3K delta · the same entry in another collection · chain A against A, TM-score 1.00
- O35904 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O35904
- Elsewhere: RCSB PDB 4XE0 · PDBe 4XE0 · UniProt O35904
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