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
- 4UWH
- Type
- protein
- Length
- 554 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
- JXM, NA
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 554 | 58% helix, 8% strand | Q8NEB9 |
Ligands and binding sites
- JXM · (8S)-9-[(2R)-2-hydroxy-2-phenylethyl]-2-(morpholin-4-yl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.63 | 0.83 | 25 | empty |
| 2 | 237 | 0.57 | 0.78 | 25 | JXM |
| 3 | 152 | 0.51 | 0.79 | 24 | empty |
| 4 | 126 | 0.44 | 0.77 | 24 | empty |
| 5 | 130 | 0.42 | 0.75 | 28 | empty |
Compared structures
- 4UWH · 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 0.95
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 4UWH · PDBe 4UWH · UniProt Q8NEB9
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