7UN0

Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-chloro-5,6-dihydrobenzo[h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor

  • Classification: HYDROLASE/INHIBITOR
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2022-04-08 Released: 2022-10-05 
  • Deposition Author(s): Gannam, Z.T.K., Jamali, H., Lolis, E., Anderson, K.S., Ellman, J.A., Bennett, A.M.
  • Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Defining the structure-activity relationship for a novel class of allosteric MKP5 inhibitors.

Gannam, Z.T.K.Jamali, H.Kweon, O.S.Herrington, J.Shillingford, S.R.Papini, C.Gentzel, E.Lolis, E.Bennett, A.M.Ellman, J.A.Anderson, K.S.

(2022) Eur J Med Chem 243: 114712-114712

  • DOI: https://doi.org/10.1016/j.ejmech.2022.114712
  • Primary Citation of Related Structures:  
    7U4O, 7U4R, 7UMU, 7UMV, 7UN0, 7UN4

  • PubMed Abstract: 

    Mitogen-activated protein kinase (MAPK) phosphatase 5 (MKP5) is responsible for regulating the activity of the stress-responsive MAPKs and has been put forth as a potential therapeutic target for a number of diseases, including dystrophic muscle disease a fatal rare disease which has neither a treatment nor cure. In previous work, we identified Compound 1 (3,3-dimethyl-1-((9-(methylthio)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl)thio)butan-2-one) as the lead compound of a novel class of MKP5 inhibitors. In this work, we explore the structure-activity relationship for inhibition of MKP5 through modifications to the scaffold and functional groups present in 1. A series of derivative compounds was designed, synthesized, and evaluated for inhibition of MKP5. In addition, the X-ray crystal structures of six enzyme-inhibitor complexes were solved, further elucidating the necessary requirements for MKP5 inhibition. We found that the parallel-displaced π-π interaction between the inhibitor three-ring core and Tyr435 is critical for modulating potency, and that modifications to the core and functionalization at the C-9 position are essential for ensuring proper positioning of the core for this interaction. These results lay the foundation from which more potent MKP5 allosteric inhibitors can be developed for potential therapeutics towards the treatment of dystrophic muscle disease.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein phosphatase 10
A, B, C, D, E
A, B, C, D, E, F
152Homo sapiensMutation(s): 0 
Gene Names: DUSP10MKP5
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6W6 (Homo sapiens)
Explore Q9Y6W6 
Go to UniProtKB:  Q9Y6W6
PHAROS:  Q9Y6W6
GTEx:  ENSG00000143507 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6W6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.078α = 90
b = 100.045β = 90
c = 135.375γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesAR66003
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122473
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI055403
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)United StatesMD122473

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Data collection
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description