Research workbench
Structure of the VPS34 kinase domain with compound 14
Analyse Structure of the VPS34 kinase domain with compound 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RSP
- Type
- protein
- Length
- 1,062 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
- 7IK
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 58% 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 | 528 | 59% helix, 9% strand | Q8NEB9 |
| B | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 534 | 57% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- 7IK · (7R,8R)-2-[(3R)-3-methylmorpholin-4-yl]-7-(propan-2-yl)-6,7-dihydropyrazolo[1,5-a]pyrazin-4(5H)-one · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.70 | 0.76 | 87 | GOL, 7IK |
| 2 | 520 | 0.64 | 0.76 | 45 | GOL, 7IK |
| 3 | 221 | 0.63 | 0.82 | 28 | empty |
| 4 | 156 | 0.61 | 0.84 | 24 | empty |
| 5 | 362 | 0.61 | 0.77 | 62 | GOL |
Interfaces
1 interface between chains.
- A–B · 636 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7RSP · Structure of the VPS34 kinase domain with compound 14 · 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 7RSP · PDBe 7RSP · UniProt Q8NEB9
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