Research workbench
Crystal structure of human PI3K-gamma in complex with benzimidazole inhibitor 5
Analyse Crystal structure of human PI3K-gamma in complex with benzimidazole inhibitor 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EDS
- Type
- protein
- Length
- 823 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
- EC
- 2.7.1.153, 2.7.11.1
- UniProt
- P48736
- Ligands
- 5MT, SO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (EC 2.7.1.153, 2.7.11.1) | protein | 823 | 45% helix, 17% strand | P48736 |
Ligands and binding sites
- 5MT · 4-azanyl-6-[[(1~{S})-1-[6-fluoranyl-1-(3-methylsulfonylphenyl)benzimidazol-2-yl]ethyl]amino]pyrimidine-5-carbonitrile · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.82 | 0.83 | 73 | SO4 |
| 2 | 444 | 0.71 | 0.82 | 63 | empty |
| 3 | 60 | 0.68 | 0.96 | 25 | empty |
| 4 | 349 | 0.66 | 0.80 | 32 | 5MT |
| 5 | 81 | 0.62 | 0.90 | 20 | empty |
Compared structures
- 5EDS · Crystal structure of human PI3K-gamma in complex with benzimidazole inhibitor 5 · 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 P48736
- Elsewhere: RCSB PDB 5EDS · PDBe 5EDS · UniProt P48736
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