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 

wwPDB Validation   3D Report Full Report



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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 22A, B326Homo sapiensMutation(s): 0 
Gene Names: PTPN22, PTPN8
EC: 3.1.3.48
Find proteins for Q9Y2R2 (Homo sapiens)
Explore Q9Y2R2 
Go to UniProtKB:  Q9Y2R2
NIH Common Fund Data Resources
PHAROS  Q9Y2R2
GTEx  ENSG00000134242
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N75
Query on N75
Download Ideal Coordinates CCD File 
A, 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		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N75Ki:  110   nM  BindingDB
N75IC50 :  259   nM  PDBBind
N75IC50:  259   nM  Binding MOAD
N75IC50:  250   nM  BindingDB
N75IC50:  259   nM  BindingDB
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


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release