Research workbench
PI4KB in complex with RAB11 and the MI358 inhibitor
Analyse PI4KB in complex with RAB11 and the MI358 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FBQ
- Type
- protein
- Length
- 629 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-kinase BETA,PHOSPHATIDYLINOSITOL 4- kinase beta; RAS-related…
- EC
- 2.7.1.67
- UniProt
- Q9UBF8, P62491
- Ligands
- 5W6, GDP
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4-kinase BETA,PHOSPHATIDYLINOSITOL 4- kinase beta (EC 2.7.1.67) | protein | 467 | 56% helix, 9% strand | Q9UBF8 |
| B | RAS-related protein rab-11A | protein | 162 | 35% helix, 28% strand | P62491 |
Ligands and binding sites
- 5W6 · ~{N}-[2-[[6-chloranyl-3-[3-[4-(hydroxymethyl)piperidin-1-yl]sulfonyl-4-methoxy-phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethyl]ethanamide · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.74 | 0.79 | 65 | 5W6 |
| 2 | 658 | 0.71 | 0.79 | 73 | GDP |
| 3 | 338 | 0.67 | 0.81 | 30 | empty |
| 4 | 169 | 0.51 | 0.78 | 31 | empty |
| 5 | 63 | 0.45 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 768 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5FBQ · PI4KB in complex with Rab11 and the MI358 Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBF8 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase beta (Q9UBF8) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9UBF8
- Every structure of UniProt P62491
- Elsewhere: RCSB PDB 5FBQ · PDBe 5FBQ · UniProt Q9UBF8 · UniProt P62491
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