6MC1

Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-(methylthio)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

An allosteric site on MKP5 reveals a strategy for small-molecule inhibition.

Gannam, Z.T.K.Min, K.Shillingford, S.R.Zhang, L.Herrington, J.Abriola, L.Gareiss, P.C.Pantouris, G.Tzouvelekis, A.Kaminski, N.Zhang, X.Yu, J.Jamali, H.Ellman, J.A.Lolis, E.Anderson, K.S.Bennett, A.M.

(2020) Sci Signal 13

  • DOI: https://doi.org/10.1126/scisignal.aba3043
  • Primary Citation of Related Structures:  
    6MC1

  • PubMed Abstract: 

    The mitogen-activated protein kinase (MAPK) phosphatases (MKPs) have been considered "undruggable," but their position as regulators of the MAPKs makes them promising therapeutic targets. MKP5 has been suggested as a potential target for the treatment of dystrophic muscle disease. Here, we identified an inhibitor of MKP5 using a p38α MAPK-derived, phosphopeptide-based small-molecule screen. We solved the structure of MKP5 in complex with this inhibitor, which revealed a previously undescribed allosteric binding pocket. Binding of the inhibitor to this pocket collapsed the MKP5 active site and was predicted to limit MAPK binding. Treatment with the inhibitor recapitulated the phenotype of MKP5 deficiency, resulting in activation of p38 MAPK and JNK. We demonstrated that MKP5 was required for TGF-β1 signaling in muscle and that the inhibitor blocked TGF-β1-mediated Smad2 phosphorylation. TGF-β1 pathway antagonism has been proposed for the treatment of dystrophic muscle disease. Thus, allosteric inhibition of MKP5 represents a therapeutic strategy against 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CJA
Query on CJA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
H [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one
C17 H20 N2 O S3
ZVUPMFXOKKTVQT-UHFFFAOYSA-N
DTT
Query on DTT

Download Ideal Coordinates CCD File 
I [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.11α = 90
b = 129.39β = 91.81
c = 83.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United States5T32AI055403-12
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesAR066003

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-09-09
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description