Research workbench
The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with pik-90
Analyse The crystal structure of the drosophila class III PI3-kinase VPS34 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X6I
- Type
- protein
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotidylinositol 3 kinase 59F
- EC
- 2.7.1.137, 2.7.1.153, 2.7.1.154
- UniProt
- Q9W1M7
- Ligands
- 090
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotidylinositol 3 kinase 59F (EC 2.7.1.137, 2.7.1.153, 2.7.1.154) | protein | 546 | 56% helix, 7% strand | Q9W1M7 |
| B | Phosphotidylinositol 3 kinase 59F (EC 2.7.1.137, 2.7.1.153, 2.7.1.154) | protein | 544 | 56% helix, 9% strand | Q9W1M7 |
Ligands and binding sites
- 090 · N-(2,3-dihydro-7,8-dimethoxyimidazo[1,2-C] quinazolin-5-yl)nicotinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.70 | 0.84 | 37 | 090 |
| 2 | 748 | 0.69 | 0.76 | 77 | empty |
| 3 | 308 | 0.65 | 0.80 | 31 | 090 |
| 4 | 247 | 0.63 | 0.82 | 24 | empty |
| 5 | 266 | 0.61 | 0.80 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1618 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2X6I · The crystal structure of the drosophila class III PI3-kinase VPS34 in complex with pik-90 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9W1M7
- Elsewhere: RCSB PDB 2X6I · PDBe 2X6I · UniProt Q9W1M7
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