MolNFT v1 · #108101 · protein
Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3- methyl-2-oxo-butyl)-2-(trifluoromethyl)-3,4-dihydro-2H- PYRIMIDO(1,2-A)PYRIMIDIN-6-one: a novel potent and selective inhibitor of VPS34 for the treatment of solid tumors
4UWK · Phosphatidylinositol 3-kinase catalytic subunit type 3: “Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3- methyl-2-oxo-butyl)-2-(trifluoromethyl)-3,4-dihydro-2H…”. X-ray diffraction, 2 ligands (UJB, SO4), 6 pockets (best…
- PDB
- 4UWK
- Type
- protein
- Length
- 544 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3-kinase catalytic subunit type 3
- EC
- 2.7.1.137
- UniProt
- Q8NEB9
- Ligands
- UJB, SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 544 | 57% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- UJB · (2S)-1-[(5-chloro-2-thienyl)methyl]-8-[(3R,5R)-3,5-dimethylmorpholin-4-yl]-2-(trifluoromethyl)-3,4-dihydro-2H-pyrimido[1,2-a]pyrimidin-6-one · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.65 | 0.84 | 22 | empty |
| 2 | 256 | 0.57 | 0.78 | 33 | UJB |
| 3 | 134 | 0.47 | 0.78 | 24 | empty |
| 4 | 120 | 0.41 | 0.76 | 30 | empty |
| 5 | 90 | 0.34 | 0.74 | 19 | empty |
Compared structures
- 4UWK · Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NEB9 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8NEB9
- Elsewhere: RCSB PDB 4UWK · PDBe 4UWK · UniProt Q8NEB9
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