Research workbench
PI3K delta in complex with [(dimethylamino) METHYLDIHYDROBENZOXAZIN2METHOXYPYRIDINYL]METHANESULFONAMIDE
Analyse PI3K delta in complex with [(dimethylamino)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZAC
- Type
- protein
- Length
- 862 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
- O35904
- Ligands
- QDE
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% 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 | 862 | 48% helix, 17% strand | O35904 |
Ligands and binding sites
- QDE · ~{N}-[5-[6-[(dimethylamino)methyl]-2,3-dihydro-1,4-benzoxazin-4-yl]-2-methoxy-pyridin-3-yl]methanesulfonamide · 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 | 1142 | 0.81 | 0.82 | 74 | empty |
| 2 | 717 | 0.72 | 0.78 | 79 | empty |
| 3 | 287 | 0.68 | 0.83 | 39 | empty |
| 4 | 536 | 0.64 | 0.76 | 54 | empty |
| 5 | 317 | 0.61 | 0.78 | 35 | QDE |
Compared structures
- 6ZAC · PI3K Delta in complex with [(dimethylamino)methyldihydrobenzoxazin2methoxypyridinyl]methan… · the same entry in another collection · chain A against A, TM-score 1.00
- O35904 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O35904
- Elsewhere: RCSB PDB 6ZAC · PDBe 6ZAC · UniProt O35904
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