Research workbench
Crystal structure of PI3KALPHA in complex with the inhibitor nvp- BYL719
Analyse Crystal structure of PI3KALPHA in complex with the inhibitor nvp- BYL719 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PG6
- Type
- protein
- Length
- 1,292 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
- 2.7.1.137, 2.7.1.153, 2.7.11.1
- UniProt
- P42336, P27986
- Ligands
- 1LT, NA
- Pockets
- 19 · best druggability 0.83
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 2.7.1.137, 2.7.1.153, 2.7.11.1) | protein | 1026 | 42% helix, 19% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 266 | 61% helix, 11% strand | P27986 |
Ligands and binding sites
- 1LT · (2S)-N~1~-{4-methyl-5-[2-(1,1,1-trifluoro-2-methylpropan-2-yl)pyridin-4-yl]-1,3-thiazol-2-yl}pyrrolidine-1,2-dicarboxamide · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.83 | 0.88 | 60 | empty |
| 2 | 1161 | 0.82 | 0.83 | 90 | empty |
| 3 | 578 | 0.81 | 0.87 | 69 | empty |
| 4 | 710 | 0.81 | 0.85 | 66 | empty |
| 5 | 424 | 0.78 | 0.87 | 63 | empty |
Interfaces
1 interface between chains.
- A–B · 3453 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 7PG6 · Crystal Structure of PI3Kalpha in complex with the inhibitor NVP-BYL719 · 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 7PG6 · PDBe 7PG6 · UniProt P42336 · UniProt P27986
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