Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 7

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.198 

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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: https://doi.org/10.1021/ja308212y
  • Primary Citation of Related Structures:  
    4GE2, 4GE5, 4GE6

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 9
A, B
314Homo sapiensMutation(s): 0 
Gene Names: PTPN9
UniProt & NIH Common Fund Data Resources
Find proteins for P43378 (Homo sapiens)
Explore P43378 
Go to UniProtKB:  P43378
PHAROS:  P43378
GTEx:  ENSG00000169410 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43378
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B26

Download Ideal Coordinates CCD File 
C [auth A]N-(4-bromo-3-methylbenzoyl)-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithyl-3-{[(4-hydroxy-3-methoxyphenyl)acetyl]amino}-D-alaninamide
C42 H45 Br F2 I N6 O11 P
Binding Affinity Annotations 
IDSourceBinding Affinity
B26 Binding MOAD:  4GE6 Ki: 34 (nM) from 1 assay(s)
PDBBind:  4GE6 Ki: 34 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.137α = 77.22
b = 57.774β = 78.03
c = 66.702γ = 80.01
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description