Research workbench
Cryo-EM structure of PI3Kalpha in complex with compound 16
Analyse Cryo-EM structure of PI3Kalpha in complex with compound 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8ILR
- Type
- protein
- Length
- 1,253 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Homo sapiens
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform…
- EC
- 2.7.1.137, 2.7.1.153, 2.7.11.1
- UniProt
- P42336, P27986
- Ligands
- 7TZ
- Pockets
- 14 · best druggability 0.85
Structure
electron microscopy · resolution 3.05 · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.137, 2.7.1.153, 2.7.11.1) | protein | 977 | 39% helix, 16% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 276 | 62% helix, 8% strand | P27986 |
Ligands and binding sites
- 7TZ · N-[(2S)-1-(ethylamino)-1-oxidanylidene-3-[4-(2-quinoxalin-6-ylethynyl)phenyl]propan-2-yl]-2,3-dimethyl-quinoxaline-6-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.85 | 0.87 | 117 | empty |
| 2 | 929 | 0.83 | 0.84 | 93 | empty |
| 3 | 516 | 0.77 | 0.84 | 67 | empty |
| 4 | 158 | 0.64 | 0.86 | 22 | empty |
| 5 | 218 | 0.64 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2878 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 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
- P27986 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase regulatory subunit… · a predicted model of the same protein · chain B 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 P42336
- Every structure of UniProt P27986
- Elsewhere: RCSB PDB 8ILR · PDBe 8ILR · UniProt P42336 · UniProt P27986
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