Research workbench
Crystal structure of PI3K complex with an inhibitor
Analyse Crystal structure of PI3K complex with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XGH
- Type
- protein
- Length
- 1,270 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
- 84U, SO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% 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 | 993 | 40% helix, 18% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 277 | 61% helix, 9% strand | P27986 |
Ligands and binding sites
- 84U · 3-[(4-fluorophenyl)methylamino]-5-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol · ligand · chains A
- SO4 · Sulfate ion · ion · chains A, B
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.87 | 0.88 | 113 | empty |
| 2 | 1080 | 0.85 | 0.86 | 88 | empty |
| 3 | 431 | 0.81 | 0.89 | 63 | empty |
| 4 | 371 | 0.76 | 0.86 | 39 | empty |
| 5 | 143 | 0.66 | 0.87 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3966 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 5XGH · Crystal structure of PI3K complex with an inhibitor · the same entry in another collection · chain B against B, 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 5XGH · PDBe 5XGH · UniProt P42336 · UniProt P27986
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