MolNFT v1 · #121826 · protein
The crystal structure of PI3KDELTA with compound 32
5I6U · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “The crystal structure of PI3KDELTA with compound 32”. X-ray diffraction, 1 ligand (68R), 11 pockets (best druggability 0.81). MolNFT v1 #121826 on GenesisL1: 3D structure…
- PDB
- 5I6U
- 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
- EC
- 2.7.1.153
- UniProt
- O35904
- Ligands
- 68R
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% 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 | 816 | 43% helix, 17% strand | O35904 |
Ligands and binding sites
- 68R · 2-[(1S)-1-({6-amino-5-[(1H-pyrazol-4-yl)ethynyl]pyrimidin-4-yl}amino)ethyl]-5-chloro-3-phenylquinazolin-4(3H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.81 | 0.82 | 77 | empty |
| 2 | 878 | 0.72 | 0.76 | 100 | empty |
| 3 | 79 | 0.71 | 0.95 | 27 | empty |
| 4 | 254 | 0.64 | 0.82 | 36 | empty |
| 5 | 349 | 0.63 | 0.79 | 41 | empty |
Compared structures
- 5I6U · The crystal structure of PI3Kdelta with compound 32 · 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 5I6U · PDBe 5I6U · UniProt O35904
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