Research workbench
Crystal structure of human PIK3C3 in complex with 3-[4-(4- MORPHOLINYL)THIENO[3,2-D]PYRIMIDIN-2-yl]-phenol
Analyse Crystal structure of human PIK3C3 in complex with 3-[4-(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LS8
- Type
- protein
- Length
- 1,069 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3-kinase catalytic subunit type 3
- EC
- 2.7.1.137
- UniProt
- Q8NEB9
- Ligands
- AJZ, CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 547 | 59% helix, 9% strand | Q8NEB9 |
| B | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 522 | 58% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- AJZ · 3-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.77 | 0.79 | 121 | AJZ, GOL |
| 2 | 176 | 0.63 | 0.84 | 22 | empty |
| 3 | 186 | 0.62 | 0.83 | 23 | empty |
| 4 | 201 | 0.54 | 0.79 | 30 | empty |
| 5 | 144 | 0.49 | 0.79 | 29 | CL |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3LS8 · Crystal structure of human PIK3C3 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NEB9 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase catalytic subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8NEB9
- Elsewhere: RCSB PDB 3LS8 · PDBe 3LS8 · UniProt Q8NEB9
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