Research workbench
PI3K delta in complex with 1BENZYLN[5(3,6DIHYDRO2HPYRAN4YL) 2METHOXYPYRIDIN3YL]2METHYL1HIMIDAZOLE4SULFONAMIDE
Analyse PI3K delta in complex with 1BENZYLN[5(3,6DIHYDRO2HPYRAN4YL)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q74
- Type
- protein
- Length
- 854 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
- HKN
- Pockets
- 14 · best druggability 0.82
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 | 854 | 47% helix, 18% strand | O35904 |
Ligands and binding sites
- HKN · ~{N}-[5-(3,6-dihydro-2~{H}-pyran-4-yl)-2-methoxy-pyridin-3-yl]-2-methyl-1-(phenylmethyl)imidazole-4-sulfonamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.82 | 0.83 | 89 | empty |
| 2 | 262 | 0.68 | 0.84 | 34 | empty |
| 3 | 405 | 0.65 | 0.79 | 41 | empty |
| 4 | 345 | 0.61 | 0.78 | 40 | HKN |
| 5 | 352 | 0.56 | 0.75 | 27 | empty |
Compared structures
- 6Q74 · PI3K delta in complex with 1benzylN[5(3,6dihydro2Hpyran4yl)2methoxypyridin3yl]2methyl1Himi… · 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 6Q74 · PDBe 6Q74 · UniProt O35904
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