Research workbench
mPI3Kd in complex with compound 7
Analyse mPI3Kd in complex with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OIS
- Type
- protein
- Length
- 827 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mus musculus
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
- EC
- 2.7.1.137, 2.7.1.153
- UniProt
- O35904
- Ligands
- VEW, NA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.137, 2.7.1.153) | protein | 827 | 46% helix, 18% strand | O35904 |
Ligands and binding sites
- VEW · N-[5-[2-[(1S)-1-cyclopropylethyl]-7-[(3-methylsulfonylphenyl)sulfamoyl]-1-oxidanylidene-3H-isoindol-5-yl]-4-methyl-1,3-thiazol-2-yl]ethanamide · ligand · chains AAA
- NA · Sodium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.81 | 0.82 | 108 | empty |
| 2 | 416 | 0.75 | 0.84 | 62 | empty |
| 3 | 302 | 0.63 | 0.80 | 36 | NA, VEW |
| 4 | 369 | 0.62 | 0.77 | 35 | empty |
| 5 | 264 | 0.55 | 0.77 | 33 | empty |
Compared structures
- O35904 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain AAA 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 7OIS · PDBe 7OIS · UniProt O35904
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