Research workbench
Crystal structure of mouse PI3 kinase delta in complex with GSK2269557
Analyse Crystal structure of mouse PI3 kinase delta in complex with GSK2269557 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AE8
- Type
- protein
- Length
- 856 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
- EC
- 2.7.1.137, 2.7.1.153
- UniProt
- O35904
- Ligands
- VVX
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.137, 2.7.1.153) | protein | 856 | 45% helix, 19% strand | O35904 |
Ligands and binding sites
- VVX · 6-(1H-Indol-4-yl)-4-(5-{[4-(1-methylethyl)-1-piperazinyl]methyl}-1,3-oxazol-2-yl)-1H-indazole · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.83 | 0.84 | 82 | empty |
| 2 | 1089 | 0.73 | 0.76 | 102 | empty |
| 3 | 306 | 0.70 | 0.84 | 53 | empty |
| 4 | 264 | 0.62 | 0.80 | 36 | VVX |
| 5 | 67 | 0.54 | 0.86 | 20 | empty |
Compared structures
- 5AE8 · Crystal structure of mouse PI3 kinase delta in complex with GSK2269557 · the same entry in another collection · chain A against A, TM-score 1.00
- O35904 · 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 0.98
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 O35904
- Elsewhere: RCSB PDB 5AE8 · PDBe 5AE8 · UniProt O35904
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