MolNFT v1 · #118972 · protein
Discovery of IMIDAZO[1,2-a]-pyridine inhibitors of pan-PI3 kinases that are efficacious in a mouse xenograft model
5FI4 · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Discovery of IMIDAZO[1,2-a]-pyridine inhibitors of pan-PI3 kinases that are efficacious in a mouse xenograft…”. X-ray diffraction, 1 ligand (5XV), 16 pockets (best…
- PDB
- 5FI4
- Type
- protein
- Length
- 1,258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform…
- EC
- 2.7.1.153, 2.7.11.1
- UniProt
- P42336, P27986
- Ligands
- 5XV
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153, 2.7.11.1) | protein | 1009 | 40% helix, 18% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 249 | 66% helix, 9% strand | P27986 |
Ligands and binding sites
- 5XV · ~{N}-[6-[5-azanyl-6-[(2~{S})-1,1,1-tris(fluoranyl)propan-2-yl]oxy-pyrazin-2-yl]imidazo[1,2-a]pyridin-2-yl]ethanamide · ligand · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.86 | 0.90 | 98 | GOL |
| 2 | 1061 | 0.84 | 0.85 | 87 | empty |
| 3 | 227 | 0.77 | 0.91 | 31 | empty |
| 4 | 364 | 0.70 | 0.82 | 59 | empty |
| 5 | 419 | 0.68 | 0.80 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 3440 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5FI4 · Discovery of imidazo[1,2-a]-pyridine inhibitors of pan-PI3 kinases that are efficacious… · the same entry in another collection · chain A against A, TM-score 1.00
- P42336 · 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 0.99
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 P42336
- Every structure of UniProt P27986
- Elsewhere: RCSB PDB 5FI4 · PDBe 5FI4 · UniProt P42336 · UniProt P27986
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