7VCE

Structural studies of human inositol monophosphatase-1 inhibition by ebselen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen.

Abuhammad, A.Laurieri, N.Rice, A.Lowe, E.D.Singh, N.Naser, S.M.Ratrout, S.S.Churchill, G.C.

(2023) J Biomol Struct Dyn : 1-13

  • DOI: https://doi.org/10.1080/07391102.2023.2176925
  • Primary Citation of Related Structures:  
    7VCE

  • PubMed Abstract: 

    Bipolar disorder is a major psychiatric disorder associated with cognitive impairment and a high suicide rate. Frontline therapy for this condition includes lithium (Li + )-containing treatments that can exert severe side effects. One target of Li + is inositol monophosphatase-1 (IMPase1); inhibition of IMPase1 through small-molecule compounds may provide an alternative treatment for bipolar disorder. One such compound is the anti-inflammatory drug ebselen, which is well tolerated and safe; however, ebselen's exact mechanism of action in IMPase1 inhibition is not fully understood, preventing rational design of IMPase1 inhibitors. To fill this gap, we performed crystallographic and biochemical studies to investigate how ebselen inhibits IMPase1. We obtained a structure of IMPase1 in space group P 2 1 after treatment with ebselen that revealed three key active-site loops (residues 33-44, 70-79, and 161-165) that are either disordered or in multiple conformations, supporting a hypothesis whereby dynamic conformational changes may be important for catalysis and ebselen inhibition. Using the thermal shift assay, we confirmed that ebselen significantly destabilizes the enzyme. Molecular docking suggests that ebselen could bind in the vicinity of His217. Investigation of the role of IMPase1 residues His217 and Cys218 suggests that inhibition of IMPase1 by ebselen may not be mediated via covalent modification of the active-site cysteine (Cys218) and is not affected by the covalent modification of other cysteine residues in the structure. Our results suggest that effects previously ascribed to ebselen-dependent inhibition likely result from disruption of essential active-site architecture, preventing activation of the IMPase1-Mg 2+ complex.Communicated by Ramaswamy H. Sarma.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol monophosphatase 1
A, B
274Homo sapiensMutation(s): 0 
Gene Names: IMPA1IMPA
EC: 3.1.3.25 (PDB Primary Data), 3.1.3.94 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P29218 (Homo sapiens)
Explore P29218 
Go to UniProtKB:  P29218
PHAROS:  P29218
GTEx:  ENSG00000133731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29218
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.29α = 90
b = 75.72β = 95.6
c = 57.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary