Research workbench
Structure of the VPS34 kinase domain with compound 5
Analyse Structure of the VPS34 kinase domain with compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RSV
- Type
- protein
- Length
- 1,063 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
- 7IQ, NA
- Pockets
- 12 · best druggability 0.66
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 | 529 | 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
- 7IQ · (5as,8ar,9s)-2-[(3R)-3-methylmorpholin-4-yl]-5,5A,6,7, 8,8A-hexahydro-4H-cyclopenta[e]pyrazolo[1,5-a]pyrazin-4-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.66 | 0.86 | 20 | empty |
| 2 | 190 | 0.62 | 0.83 | 22 | NA |
| 3 | 456 | 0.62 | 0.76 | 48 | 7IQ, GOL |
| 4 | 455 | 0.62 | 0.76 | 41 | 7IQ, GOL |
| 5 | 389 | 0.57 | 0.75 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 618 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7RSV · Structure of the VPS34 kinase domain with compound 5 · 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 7RSV · PDBe 7RSV · UniProt Q8NEB9
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