6M89

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of Inositol Polyphosphate Kinases by Quercetin and Related Flavonoids: A Structure-Activity Analysis.

Gu, C.Stashko, M.A.Puhl-Rubio, A.C.Chakraborty, M.Chakraborty, A.Frye, S.V.Pearce, K.H.Wang, X.Shears, S.B.Wang, H.

(2019) J. Med. Chem. 62: 1443-1454

  • DOI: 10.1021/acs.jmedchem.8b01593
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dietary flavonoids inhibit certain protein kinases and phospholipid kinases by competing for their ATP-binding sites. These nucleotide pockets have structural elements that are well-conserved in two human small-molecule kinases, inositol hexakisphosp ...

    Dietary flavonoids inhibit certain protein kinases and phospholipid kinases by competing for their ATP-binding sites. These nucleotide pockets have structural elements that are well-conserved in two human small-molecule kinases, inositol hexakisphosphate kinase (IP6K) and inositol polyphosphate multikinase (IPMK), which synthesize multifunctional inositol phosphate cell signals. Herein, we demonstrate that both kinases are inhibited by quercetin and 16 related flavonoids; IP6K is the preferred target. Relative inhibitory activities were rationalized by X-ray analysis of kinase/flavonoid crystal structures; this detailed structure-activity analysis revealed hydrophobic and polar ligand/protein interactions, the degree of flexibility of key amino acid side chains, and the importance of water molecules. The seven most potent IP6K inhibitors were incubated with intact HCT116 cells at concentrations of 2.5 μM; diosmetin was the most selective and effective IP6K inhibitor (>70% reduction in activity). Our data can instruct on pharmacophore properties to assist the future development of inositol phosphate kinase inhibitors. Finally, we propose that dietary flavonoids may inhibit IP6K activity in cells that line the gastrointestinal tract.


    Organizational Affiliation

    Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States.,Department of Biochemistry and Molecular Biology, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5G 1L6, Canada.,Cancer institute, the Affiliated Hospital of Qingdao University, Qingdao Cancer Institute and School of Basic Medicine, Qingdao University, 266021, Qingdao, China.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada. sli@uwo.ca.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.,Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.,Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States.,Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.,Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico.,Departments of Biochemistry and Molecular Genetics, MaRS Centre, West Tower, Floor 16, Toronto, ON, M5G 1M1, Canada.,Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States.,Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioner's Road East, London, ON, N6C 2V5, Canada. sli@uwo.ca.,Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol polyphosphate multikinase,Inositol polyphosphate multikinase
A
261Homo sapiensMutation(s): 0 
Gene Names: IPMK (IMPK)
EC: 2.7.1.140, 2.7.1.151, 2.7.1.153
Find proteins for Q8NFU5 (Homo sapiens)
Go to Gene View: IPMK
Go to UniProtKB:  Q8NFU5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download SDF File 
Download CCD File 
A
3,5,7,3',4'-PENTAHYDROXYFLAVONE
QUERCETIN
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.174 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.956α = 90.00
b = 77.956β = 90.00
c = 84.468γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-21 
  • Released Date: 2019-01-23 
  • Deposition Author(s): Wang, H., Shears, S.B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIAES080046-29

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence