8V73 | pdb_00008v73

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 9

• PDB DOI: https://doi.org/10.2210/pdb8V73/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-04 Released: 2024-12-11 
• Deposition Author(s): Wang, H., Shears, S.B.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Structural Rationalization of IPMK Inhibitor Potency.

Wang, H., Shears, S.B., Blind, R.D.

(2025) J Med Chem 68: 24316-24325

• PubMed: 41237254 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c02314
• Primary Citation Related Structures: 
  8V6W, 8V6X, 8V6Y, 8V6Z, 8V70, 8V71, 8V72, 8V73, 8V74, 8V75, 8V76, 8V77, 8V78, 8V79


• PubMed Abstract: 
  

  Inositol polyphosphate multikinase (IPMK) is a kinase linked to several cancers; recent development of a large panel of ATP-competitive inhibitors has reinvigorated enthusiasm for targeting IPMK. However, the structural basis for how these inhibitors achieve high potency is unknown. Herein, we report 14 novel cocrystal structures (1.7-2.0 resolution) of human IPMK kinase domain with these inhibitors. We also apply a radiolabeled assay and isothermal titration calorimetry that permit high-confidence IC ₅₀ and K _D value determinations. The structures reveal a pocket in the ATP-binding site engaged by the most potent inhibitors. Two ordered waters also participate in hydrogen-bonding networks associated with the most potent inhibitors. In addition to providing the molecular basis for observed increases in potency and selectivity, the data presented here provide a toolbelt of 14 novel inhibitor-bound structures of human IPMK that can serve as a reference for all future IPMK structure-based inhibitor development efforts.

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Organizational Affiliation: 
• Molecular and Cellular Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina 27709, United States.
Department of Medicine, Division of Diabetes, Endocrinology & Metabolism, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.
Departments of Biochemistry & Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.18 kDa 
• Atom Count: 2,126 
• Modeled Residue Count: 237 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol polyphosphate multikinase	A	261	Homo sapiens	Mutation(s): 0  Gene Names: IPMK, IMPK EC: 2.7.1.140 (PDB Primary Data), 2.7.1.151 (PDB Primary Data), 2.7.1.153 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFU5 (Homo sapiens) Explore Q8NFU5  Go to UniProtKB:  Q8NFU5
PHAROS:  Q8NFU5 GTEx:  ENSG00000151151

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YIG (Subject of Investigation/LOI)	B [auth A]	(5P)-3-(4-phenoxyphenyl)-5-(1H-tetrazol-5-yl)-2,1-benzoxazole C20 H13 N5 O2 RMVHXXZAXAMVLU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.808	α = 90
b = 77.808	β = 90
c = 84.899	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Wang, H., Shears, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIAES080046

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-11-26
  Changes: Database references
• Version 1.2: 2025-12-10
  Changes: Database references