8U5M

Structure of Sts-1 HP domain with rebamipide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rebamipide and Derivatives are Potent, Selective Inhibitors of Histidine Phosphatase Activity of the Suppressor of T Cell Receptor Signaling Proteins.

Aziz, F.Reddy, K.Fernandez Vega, V.Dey, R.Hicks, K.A.Rao, S.Jordan, L.O.Smith, E.Shumate, J.Scampavia, L.Carpino, N.Spicer, T.P.French, J.B.

(2024) J Med Chem 67: 1949-1960

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01763
  • Primary Citation of Related Structures:  
    8U5M, 8U7E

  • PubMed Abstract: 

    The suppressor of T cell receptor signaling (Sts) proteins are negative regulators of immune signaling. Genetic inactivation of these proteins leads to significant resistance to infection. From a 590,000 compound high-throughput screen, we identified the 2-( 1H )-quinolinone derivative, rebamipide, as a putative inhibitor of Sts phosphatase activity. Rebamipide, and a small library of derivatives, are competitive, selective inhibitors of Sts-1 with IC 50 values from low to submicromolar. SAR analysis indicates that the quinolinone, the acid, and the amide moieties are all essential for activity. A crystal structure confirmed the SAR and reveals key interactions between this class of compound and the protein. Although rebamipide has poor cell permeability, we demonstrated that a liposomal preparation can inactivate the phosphatase activity of Sts-1 in cells. These studies demonstrate that Sts-1 enzyme activity can be pharmacologically inactivated and provide foundational tools and insights for the development of immune-enhancing therapies that target the Sts proteins.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York 11790, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-associated and SH3 domain-containing protein B
A, B, C, D, E
A, B, C, D, E, F
287Homo sapiensMutation(s): 0 
Gene Names: UBASH3B
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF42 (Homo sapiens)
Explore Q8TF42 
Go to UniProtKB:  Q8TF42
GTEx:  ENSG00000154127 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TF42
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.65α = 90
b = 122.274β = 112.41
c = 99.588γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI141592

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references