Research workbench
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
Analyse Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UWL
- Type
- protein
- Length
- 543 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
- 7A5, SO4
- Pockets
- 6 · best druggability 0.62
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 | 543 | 57% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- 7A5 · (8S)-2-[(3R)-3-methylmorpholin-4-yl]-9-(3-methyl-2-oxobutyl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · 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 | 172 | 0.62 | 0.84 | 23 | SO4 |
| 2 | 228 | 0.59 | 0.79 | 24 | SO4, 7A5 |
| 3 | 143 | 0.46 | 0.77 | 23 | empty |
| 4 | 56 | 0.30 | 0.76 | 10 | empty |
| 5 | 53 | 0.30 | 0.75 | 11 | empty |
Compared structures
- 4UWL · 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 4UWL · PDBe 4UWL · UniProt Q8NEB9
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