MolNFT v1 · #86744 · protein
Discovery and optimization of pyrimidone indoline amide PI3KBETA inhibitors for the treatment of phosphatase and tensin homologue (pten)-deficient cancers
4BFR · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic S…: “Discovery and optimization of pyrimidone indoline amide PI3KBETA inhibitors for the treatment of phosphatase…”. X-ray diffraction, 1 ligand (J82), 20 pockets (best…
- PDB
- 4BFR
- Type
- protein
- Length
- 1,691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic S subunit beta isoform
- EC
- 2.7.1.153
- UniProt
- Q8BTI9
- Ligands
- J82
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic S subunit beta isoform (EC 2.7.1.153) | protein | 855 | 46% helix, 15% strand | Q8BTI9 |
| B | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic S subunit beta isoform (EC 2.7.1.153) | protein | 836 | 46% helix, 17% strand | Q8BTI9 |
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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.81 | 0.83 | 71 | empty |
| 2 | 1019 | 0.78 | 0.80 | 80 | empty |
| 3 | 542 | 0.71 | 0.80 | 63 | empty |
| 4 | 650 | 0.69 | 0.78 | 75 | empty |
| 5 | 488 | 0.69 | 0.80 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 1629 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4BFR · Discovery and Optimization of Pyrimidone Indoline Amide PI3Kbeta Inhibitors for the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BTI9 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain B 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 Q8BTI9
- Elsewhere: RCSB PDB 4BFR · PDBe 4BFR · UniProt Q8BTI9
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