MolNFT v1 · #113712 · protein
Crystal structure of VPS34 in complex with (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, processed with the crystaldirect automated mounting and cryo-cooling technology
5ANL · Phosphatidylinositol 3-kinase catalytic subunit type 3: “Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- methylmorpholin-4-yl)-1-(3-methyl-2-oxo…”. X-ray diffraction, 1 ligand (RBQ), 6 pockets (best druggability 0.64).…
- PDB
- 5ANL
- 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
- RBQ
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 56% 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 | 56% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- RBQ · (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one · ligand · 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 | 146 | 0.64 | 0.86 | 22 | empty |
| 2 | 246 | 0.57 | 0.78 | 30 | RBQ |
| 3 | 149 | 0.46 | 0.77 | 19 | empty |
| 4 | 94 | 0.39 | 0.76 | 21 | empty |
| 5 | 50 | 0.32 | 0.78 | 16 | empty |
Compared structures
- 5ANL · Crystal structure of VPS34 in complex with (2S)-8-((3R)-3… · 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 5ANL · PDBe 5ANL · UniProt Q8NEB9
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