MolNFT v1 · #139463 · protein
Crystal structure of PI3K complex with an inhibitor
5XGJ · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Crystal structure of PI3K complex with an inhibitor”. X-ray diffraction, 2 ligands (84X, SO4), 16 pockets (best druggability 0.87). MolNFT v1 #139463 on GenesisL1: 3D…
- PDB
- 5XGJ
- 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
- 84X, SO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 46% 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 | 980 | 41% helix, 19% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 278 | 62% helix, 10% strand | P27986 |
Ligands and binding sites
- 84X · 3-(4-morpholin-4-ylfuro[3,2-d]pyrimidin-2-yl)-5-[(phenylmethyl)amino]phenol · ligand · chains A
- SO4 · Sulfate ion · ion · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.87 | 0.89 | 119 | empty |
| 2 | 1068 | 0.85 | 0.86 | 93 | empty |
| 3 | 419 | 0.80 | 0.88 | 58 | empty |
| 4 | 342 | 0.75 | 0.86 | 37 | empty |
| 5 | 169 | 0.68 | 0.87 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 4027 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5XGJ · Crystal structure of PI3K complex with an inhibitor · 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 5XGJ · PDBe 5XGJ · UniProt P42336 · UniProt P27986
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