9HHM | pdb_00009hhm

Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with HH5129

• PDB DOI: https://doi.org/10.2210/pdb9HHM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-22 Released: 2025-12-03 
• Deposition Author(s): Klima, M., Boura, E.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Compounds mimicking the Michaelis-Menten transition state of the phosphatidylinositol 4-kinase.

Hrebabecky, H., Klima, M., Dejmek, M., Krupa, P., Fernandez, M.R., Davidova, E., Benysek, J., Martinez-Seara, H., Rozycki, B., Boura, E., Nencka, R.

(2026) Bioorg Med Chem 139: 118666-118666

• PubMed: 42086018 
• DOI: https://doi.org/10.1016/j.bmc.2026.118666
• Primary Citation Related Structures: 
  9HHM


• PubMed Abstract: 
  

  Phosphatidylinositol 4-kinases (PI4Ks) are crucial enzymes in lipid signaling responsible for generating phosphatidylinositol-4-phosphate (PI4P). Although the ATP-binding site of PI4Ks has been extensively studied, the structural characterization of their natural substrate, phosphatidylinositol (PI), bound to the enzyme remains elusive. In this study, we synthesized novel non-hydrolyzable Michaelis-Menten transition state mimetics in which the ADP molecule is covalently linked to inositol-4-phosphate or simple phosphatidylinositol-4-phosphate via a methylene or ethylene bridge. During our synthesis efforts, we successfully addressed the significantly limited reactivity at position 4 of inositols by utilizing P(III) phosphorus reagents, which proved crucial for the synthesis of these mimetics. For the simplest ADP-C-4PI analogue, we obtained a crystal structure of PI4K2B, which can be used to understand how these phospholipids are phosphorylated on membrane surfaces.

---

Organizational Affiliation: 
• Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo náměstí 542/2, 166 10 Prague, Czech Republic.
Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo náměstí 542/2, 166 10 Prague, Czech Republic. Electronic address: [e-mail].
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo náměstí 542/2, 166 10 Prague, Czech Republic. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.56 kDa 
• Atom Count: 7,458 
• Modeled Residue Count: 897 
• Deposited Residue Count: 1,034 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase type 2-beta,Endolysin	A, B	517	Homo sapiens, Tequatrovirus T4	Mutation(s): 0  Gene Names: PI4K2B EC: 2.7.1.67 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for Q8TCG2 (Homo sapiens) Explore Q8TCG2  Go to UniProtKB:  Q8TCG2
PHAROS:  Q8TCG2 GTEx:  ENSG00000038210
UniProt Groups	P00720Q8TCG2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IVA (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1~{S},2~{S},4~{S},5~{R})-6-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]methyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxycyclohexane-1,2,3,4,5-pentol C17 H25 N5 O17 P3 SXKKMVQPOLWBJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.24	α = 90
b = 105.24	β = 90
c = 211.64	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Klima, M., Boura, E.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release
  
• Version 1.1: 2026-05-20
  Changes: Database references