Research workbench
Human PI3KDELTA in complex with compound 3C
Analyse Human PI3KDELTA in complex with compound 3C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LM2
- Type
- protein
- Length
- 1,104 residues
- Chains
- 2
- 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
- O00329, P27986
- Ligands
- Y5Y, SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% 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 | 935 | 44% helix, 19% strand | O00329 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 169 | 86% helix, 0% strand | P27986 |
Ligands and binding sites
- Y5Y · cyclopropyl[(3S)-3-{[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]amino}pyrrolidin-1-yl]methanone · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.84 | 0.85 | 84 | SO4 |
| 2 | 1109 | 0.83 | 0.84 | 114 | EDO |
| 3 | 301 | 0.67 | 0.82 | 46 | empty |
| 4 | 260 | 0.61 | 0.80 | 36 | Y5Y |
| 5 | 109 | 0.58 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2334 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
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 O00329
- Every structure of UniProt P27986
- Elsewhere: RCSB PDB 7LM2 · PDBe 7LM2 · UniProt O00329 · UniProt P27986
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