MolNFT v1 · #186853 · protein
Structure of the VPS34 kinase domain with compound 14
7RSJ · Phosphatidylinositol 3-kinase catalytic subunit type 3: “Structure of the VPS34 kinase domain with compound 14”. X-ray diffraction, 2 ligands (7IH, NA), 5 pockets (best druggability 0.62). MolNFT v1 #186853 on GenesisL1: 3D…
- PDB
- 7RSJ
- Type
- protein
- Length
- 545 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
- 7IH, NA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 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 | 545 | 58% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- 7IH · N-{4-[(7R,8R)-4-oxo-7-(propan-2-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl]pyridin-2-yl}cyclopropanecarboxamide · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.62 | 0.84 | 23 | empty |
| 2 | 215 | 0.54 | 0.77 | 27 | 7IH, GOL |
| 3 | 223 | 0.53 | 0.77 | 28 | empty |
| 4 | 81 | 0.37 | 0.77 | 21 | empty |
| 5 | 54 | 0.31 | 0.76 | 20 | empty |
Compared structures
- 7RSJ · 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 0.96
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 7RSJ · PDBe 7RSJ · UniProt Q8NEB9
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