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Water network determines selectivity for a series of pyrimidone indoline amide PI3KBETA inhibitors over PI3K-delta
Analyse Water network determines selectivity for a series of pyrimidone indoline amide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V0I
- Type
- protein
- Length
- 1,551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform
- EC
- 2.7.1.153
- UniProt
- O35904
- Ligands
- J82
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) | protein | 759 | 48% helix, 16% strand | O35904 |
| B | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) | protein | 792 | 46% helix, 18% strand | O35904 |
Ligands and binding sites
- J82 · 2-[2-(2-methyl-2,3-dihydro-indol-1-yl)-2-oxo-ethyl]-6-morpholin-4-yl-3H-pyrimidin-4-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.81 | 0.83 | 72 | empty |
| 2 | 791 | 0.81 | 0.84 | 67 | empty |
| 3 | 721 | 0.70 | 0.77 | 75 | empty |
| 4 | 529 | 0.69 | 0.79 | 66 | empty |
| 5 | 289 | 0.69 | 0.83 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 821 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4V0I · Water Network Determines Selectivity for a Series of Pyrimidone Indoline Amide PI3KBeta… · 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 4V0I · PDBe 4V0I · UniProt O35904
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