MolNFT v1 · #118766 · protein

PI4KB in complex with RAB11 and the MI364 inhibitor

5FBV · Phosphatidylinositol 4-kinase BETA,PHOSPHATIDYLINOSITOL 4…: “PI4KB in complex with RAB11 and the MI364 inhibitor”. X-ray diffraction, 2 ligands (5W3, GSP), 8 pockets (best druggability 0.74). MolNFT v1 #118766 on GenesisL1: 3D…

PDB: 5FBV
Type: protein
Length: 632 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: 5W3, GSP
Pockets: 8 · 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	465	55% helix, 9% strand	Q9UBF8
B	RAS-related protein rab-11A	protein	167	34% helix, 27% strand	P62491

Ligands and binding sites

5W3 · ~{N}-[2-[[6-chloranyl-3-[3-(2-hydroxyethylsulfamoyl)-4-methoxy-phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethy l]ethanamide · ligand · chains A
GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	810	0.74	0.78	64	5W3
2	403	0.69	0.81	57	GSP
3	396	0.68	0.80	38	empty
4	75	0.46	0.82	18	empty
5	86	0.41	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 632 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5FBV · PI4KB in complex with Rab11 and the MI364 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 0.98

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 Q9UBF8
Every structure of UniProt P62491
Elsewhere: RCSB PDB 5FBV · PDBe 5FBV · UniProt Q9UBF8 · UniProt P62491

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