Research workbench
The crystal structure of the murine class ia pi 3-kinase P110DELTA in complex with SW30.
Analyse The crystal structure of the murine class ia pi 3-kinase P110DELTA in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WXI
- Type
- protein
- Length
- 815 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform
- EC
- 2.7.1.153
- UniProt
- Q3UDT3
- Ligands
- S30
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) | protein | 815 | 47% helix, 18% strand | Q3UDT3 |
Ligands and binding sites
- S30 · 2-{[4-amino-3-(3-hydroxyprop-1-yn-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]methyl}-5-methyl-3-(2-methylphenyl)quinazolin-4(3H)-one · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.80 | 0.82 | 82 | empty |
| 2 | 396 | 0.73 | 0.83 | 54 | empty |
| 3 | 919 | 0.72 | 0.77 | 102 | empty |
| 4 | 338 | 0.64 | 0.79 | 34 | S30 |
| 5 | 101 | 0.49 | 0.81 | 26 | empty |
Compared structures
- 2WXI · The crystal structure of the murine class IA PI 3-kinase p110delta in complex with SW30. · 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 Q3UDT3
- Elsewhere: RCSB PDB 2WXI · PDBe 2WXI · UniProt Q3UDT3
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