4GE5

Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Highly Selective and Potent PTP-MEG2 Inhibitor with Therapeutic Potential for Type 2 Diabetes.

Zhang, S.Liu, S.Tao, R.Wei, D.Chen, L.Shen, W.Yu, Z.H.Wang, L.Jones, D.R.Dong, X.C.Zhang, Z.Y.

(2012) J.Am.Chem.Soc. 134: 18116-18124

  • DOI: 10.1021/ja308212y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein tyrosine phosphatases (PTPs) constitute a large family of signaling enzymes that control the cellular levels of protein tyrosine phosphorylation. A detailed understanding of PTP functions in normal physiology and in pathogenic conditions has ...

    Protein tyrosine phosphatases (PTPs) constitute a large family of signaling enzymes that control the cellular levels of protein tyrosine phosphorylation. A detailed understanding of PTP functions in normal physiology and in pathogenic conditions has been hampered by the absence of PTP-specific, cell-permeable small-molecule agents. We present a stepwise focused library approach that transforms a weak and general non-hydrolyzable pTyr mimetic (F(2)Pmp, phosphonodifluoromethyl phenylalanine) into a highly potent and selective inhibitor of PTP-MEG2, an antagonist of hepatic insulin signaling. The crystal structures of the PTP-MEG2-inhibitor complexes provide direct evidence that potent and selective PTP inhibitors can be obtained by introducing molecular diversity into the F(2)Pmp scaffold to engage both the active site and unique nearby peripheral binding pockets. Importantly, the PTP-MEG2 inhibitor possesses highly efficacious cellular activity and is capable of augmenting insulin signaling and improving insulin sensitivity and glucose homeostasis in diet-induced obese mice. The results indicate that F(2)Pmp can be converted into highly potent and selective PTP inhibitory agents with excellent in vivo efficacy. Given the general nature of the approach, this strategy should be applicable to other members of the PTP superfamily.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 9
A, B
314Homo sapiensMutation(s): 0 
Gene Names: PTPN9
EC: 3.1.3.48
Find proteins for P43378 (Homo sapiens)
Go to Gene View: PTPN9
Go to UniProtKB:  P43378
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A89
Query on A89

Download SDF File 
Download CCD File 
A
N-(4-bromo-3-methylbenzoyl)-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithinamide
C30 H31 Br F2 I N4 O7 P
PSWNGHKKMCDZPT-DQEYMECFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A89IC50: 270 nM BINDINGMOAD
A89IC50: 270 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.260α = 77.55
b = 57.170β = 78.23
c = 66.422γ = 79.97
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references