Research workbench
The co-structure of 3-amino-6-(4-((1-(dimethylamino)propan-2-yl)sulfonyl)phenyl)-N-phenylpyrazine-2-carboxamide and a rationally designed PI3K-alpha mutant that mimics ATR
Analyse The co-structure of 3-amino-6-(4-((1-(dimethylamino)propan-2-yl)sulfonyl)phenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UL1
- Type
- protein
- Length
- 1,257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Homo sapiens
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform…
- EC
- 2.7.1.153, 2.7.11.1
- UniProt
- P42336, P27986
- Ligands
- 8DY
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · resolution 3 · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153, 2.7.11.1) | protein | 1000 | 41% helix, 18% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 257 | 63% helix, 12% strand | P27986 |
Ligands and binding sites
- 8DY · 3-amino-6-(4-{[(2S)-1-(dimethylamino)propan-2-yl]sulfonyl}phenyl)-N-phenylpyrazine-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.84 | 0.89 | 86 | empty |
| 2 | 673 | 0.83 | 0.88 | 62 | empty |
| 3 | 1199 | 0.82 | 0.83 | 84 | empty |
| 4 | 273 | 0.75 | 0.88 | 30 | empty |
| 5 | 257 | 0.66 | 0.83 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 3389 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5UL1 · The co-structure of 3-amino-6-(4-((1-(DIMETHYLAMINO)PROPAN-2-yl)… · the same entry in another collection · chain A against A, TM-score 1.00
- P42336 · 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 1.00
- P27986 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase regulatory subunit… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P42336
- Every structure of UniProt P27986
- Elsewhere: RCSB PDB 5UL1 · PDBe 5UL1 · UniProt P42336 · UniProt P27986
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