Research workbench
The crystal structure of the murine class ia pi 3-kinase P110DELTA in complex with gdc-0941.
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
- 2WXP
- Type
- protein
- Length
- 822 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
- GD9
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% 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 | 822 | 48% helix, 18% strand | Q3UDT3 |
Ligands and binding sites
- GD9 · 2-(1H-indazol-4-yl)-6-{[4-(methylsulfonyl)piperazin-1-yl]methyl}-4-morpholin-4-yl-thieno[3,2-d]pyrimidine · ligand · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.80 | 0.82 | 80 | empty |
| 2 | 1005 | 0.73 | 0.76 | 99 | empty |
| 3 | 285 | 0.66 | 0.82 | 37 | empty |
| 4 | 110 | 0.63 | 0.88 | 27 | empty |
| 5 | 263 | 0.59 | 0.78 | 33 | GD9 |
Compared structures
- 2WXP · The crystal structure of the murine class IA PI 3-kinase p110delta in complex with… · 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 2WXP · PDBe 2WXP · UniProt Q3UDT3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.