4J51

Cyrstal structure of protein tyrosine phosphatase Lyp catalytic domain complex with small molecular inhibitor L75N04


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Potent and Selective Small-Molecule Inhibitor for the Lymphoid-Specific Tyrosine Phosphatase (LYP), a Target Associated with Autoimmune Diseases.

He, Y.Liu, S.Menon, A.Stanford, S.Oppong, E.Gunawan, A.M.Wu, L.Wu, D.J.Barrios, A.M.Bottini, N.Cato, A.C.Zhang, Z.Y.

(2013) J Med Chem 56: 4990-5008

  • DOI: https://doi.org/10.1021/jm400248c
  • Primary Citation of Related Structures:  
    4J51

  • PubMed Abstract: 

    Lymphoid-specific tyrosine phosphatase (LYP), a member of the protein tyrosine phosphatase (PTP) family of signaling enzymes, is associated with a broad spectrum of autoimmune diseases. Herein we describe our structure-based lead optimization efforts within a 6-hydroxy-benzofuran-5-carboxylic acid series culminating in the identification of compound 8b, a potent and selective inhibitor of LYP with a K(i) value of 110 nM and more than 9-fold selectivity over a large panel of PTPs. The structure of LYP in complex with 8b was obtained by X-ray crystallography, providing detailed information about the molecular recognition of small-molecule ligands binding LYP. Importantly, compound 8b possesses highly efficacious cellular activity in both T- and mast cells and is capable of blocking anaphylaxis in mice. Discovery of 8b establishes a starting point for the development of clinically useful LYP inhibitors for treating a wide range of autoimmune disorders.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 22
A, B
326Homo sapiensMutation(s): 0 
Gene Names: PTPN22PTPN8
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R2 (Homo sapiens)
Explore Q9Y2R2 
Go to UniProtKB:  Q9Y2R2
PHAROS:  Q9Y2R2
GTEx:  ENSG00000134242 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2R2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N75
Query on N75

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-[(3-chlorophenyl)ethynyl]-2-{4-[2-(cyclopropylamino)-2-oxoethoxy]phenyl}-6-hydroxy-1-benzofuran-5-carboxylic acid
C28 H20 Cl N O6
IIURSEJMCKFEQG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
N75 BindingDB:  4J51 Ki: 110 (nM) from 1 assay(s)
IC50: min: 250, max: 259 (nM) from 2 assay(s)
Binding MOAD:  4J51 IC50: 259 (nM) from 1 assay(s)
PDBBind:  4J51 IC50: 259 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.193α = 90
b = 93.644β = 90
c = 153.498γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description