Research workbench
PI3 kinase delta in complex with 3{6[(1S,6R) 3OXABICYCLO[4.1.0]HEPTAN6YL]PYRIDIN2YL}PHENOL
Analyse PI3 kinase delta in complex with 3{6[(1S,6R)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HI2
- Type
- protein
- Length
- 860 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
- G62
- Pockets
- 12 · best druggability 0.82
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 | 860 | 48% helix, 17% strand | O35904 |
Ligands and binding sites
- G62 · 3-[6-[(1~{S},6~{R})-3-oxabicyclo[4.1.0]heptan-6-yl]pyridin-2-yl]phenol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.82 | 0.83 | 82 | empty |
| 2 | 282 | 0.69 | 0.84 | 39 | empty |
| 3 | 483 | 0.69 | 0.79 | 53 | empty |
| 4 | 357 | 0.63 | 0.79 | 44 | empty |
| 5 | 222 | 0.59 | 0.79 | 26 | G62 |
Compared structures
- 6HI2 · PI3 Kinase Delta in complex with 3{6[(1S,6R)3oxabicyclo[4.1.0]heptan6yl]pyridin2yl}phenol · 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 6HI2 · PDBe 6HI2 · UniProt O35904
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