Research workbench
The crystal structure of human VPS34 in complex with a selective and potent inhibitor
Analyse The crystal structure of human VPS34 in complex with a selective and potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ENN
- Type
- protein
- Length
- 1,057 residues
- Chains
- 2
- 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
- 5QS, NA, SO4
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 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 | 526 | 57% helix, 9% strand | Q8NEB9 |
| B | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 531 | 57% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- 5QS · 1-[[4-(cyclopropylmethyl)-5-[2-(pyridin-4-ylamino)pyrimidin-4-yl]pyrimidin-2-yl]amino]-2-methyl-propan-2-ol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.67 | 0.83 | 36 | empty |
| 2 | 230 | 0.65 | 0.83 | 31 | NA |
| 3 | 168 | 0.61 | 0.83 | 25 | NA |
| 4 | 307 | 0.59 | 0.77 | 32 | 5QS |
| 5 | 289 | 0.58 | 0.77 | 25 | 5QS |
Interfaces
1 interface between chains.
- A–B · 1036 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5ENN · The crystal structure of Human VPS34 in complex with a selective and potent inhibitor · 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 0.99
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 5ENN · PDBe 5ENN · UniProt Q8NEB9
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