Research workbench
PI3K delta in complex with METHOXY(METHYLSULFAMOYL) PYRIDINYLN(METHYLPIPERIDINYL)DIHYDROBENZOXAZINECARBOXAMIDE
Analyse PI3K delta in complex with METHOXY(METHYLSULFAMOYL)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZAA
- Type
- protein
- Length
- 859 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
- QD2
- Pockets
- 13 · best druggability 0.81
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 | 859 | 47% helix, 18% strand | O35904 |
Ligands and binding sites
- QD2 · 4-[6-methoxy-5-(methylsulfamoyl)pyridin-3-yl]-~{N}-(1-methylpiperidin-4-yl)-2,3-dihydro-1,4-benzoxazine-6-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.81 | 0.82 | 77 | empty |
| 2 | 259 | 0.70 | 0.85 | 37 | empty |
| 3 | 294 | 0.64 | 0.80 | 30 | QD2 |
| 4 | 362 | 0.62 | 0.77 | 32 | empty |
| 5 | 292 | 0.56 | 0.77 | 38 | empty |
Compared structures
- 6ZAA · PI3K Delta in complex with methoxy(methylsulfamoyl)pyridinylN(methylpiperidinyl)dihydroben… · 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 6ZAA · PDBe 6ZAA · UniProt O35904
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