Research workbench
X-ray diffraction crystal structure of the murine PI3K P110DELTA in complex with a pan inhibitor
Analyse X-ray diffraction crystal structure of the murine PI3K P110DELTA in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NGB
- Type
- protein
- Length
- 816 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
- UniProt
- Q3UDT3
- Ligands
- 8WH
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | protein | 816 | 48% helix, 18% strand | Q3UDT3 |
Ligands and binding sites
- 8WH · 3-[[4-(2-morpholin-4-yl-4-oxidanylidene-3~{H}-quinolin-8-yl)-1,2,3-triazol-1-yl]methyl]benzoic acid · 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 | 1135 | 0.81 | 0.82 | 77 | empty |
| 2 | 921 | 0.72 | 0.76 | 85 | empty |
| 3 | 318 | 0.69 | 0.82 | 44 | empty |
| 4 | 60 | 0.67 | 0.95 | 25 | empty |
| 5 | 193 | 0.57 | 0.79 | 26 | 8WH |
Compared structures
- 5NGB · X-Ray Diffraction Crystal Structure of the murine PI3K p110delta in complex with a pan… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q3UDT3
- Elsewhere: RCSB PDB 5NGB · PDBe 5NGB · UniProt Q3UDT3
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