MolNFT v1 · #125372 · protein
PI3 kinase delta in complex with N-[6-(5-methanesulfonamido-6- methoxypyridin-3-yl)-1,3-dihydro-2-benzofuran-4-yl]-2-(morpholin-4- YL)ACETAMIDE
5L72 · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “PI3 kinase delta in complex with N-[6-(5-methanesulfonamido-6…”. X-ray diffraction, 1 ligand (6PF), 12 pockets (best druggability 0.81). MolNFT v1 #125372 on GenesisL1: 3D…
- PDB
- 5L72
- Type
- protein
- Length
- 858 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
- 2.7.1.137, 2.7.1.153
- UniProt
- O35904
- Ligands
- 6PF
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.137, 2.7.1.153) | protein | 858 | 46% helix, 18% strand | O35904 |
Ligands and binding sites
- 6PF · N-[6-(5-methanesulfonamido-6-methoxypyridin-3-yl)-1,3-dihydro-2-benzofuran-4-yl]-2-(morpholin-4-yl)acetamide · 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 | 1114 | 0.81 | 0.82 | 73 | empty |
| 2 | 663 | 0.70 | 0.78 | 63 | empty |
| 3 | 287 | 0.68 | 0.83 | 34 | empty |
| 4 | 269 | 0.61 | 0.79 | 31 | 6PF |
| 5 | 433 | 0.60 | 0.75 | 52 | empty |
Compared structures
- 5L72 · PI3 kinase delta in complex with N-[6-(5-methanesulfonamido-6-methoxypyridin-3-yl)-1,3-dih… · 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 5L72 · PDBe 5L72 · UniProt O35904
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