8JBN

Vascular endothelial protein tyrosine phosphatase in complex with Cpd-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


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Literature

Fragment-Based Discovery of Novel VE-PTP Inhibitors Using Orthogonal Biophysical Techniques.

Asano, W.Yamanaka, K.Ohara, Y.Uhara, T.Doi, S.Orita, T.Iwanaga, T.Adachi, T.Fujioka, S.Akaki, T.Ikegashira, K.Hantani, Y.

(2023) Biochemistry 62: 2161-2169

  • DOI: https://doi.org/10.1021/acs.biochem.3c00079
  • Primary Citation of Related Structures:  
    8JBN, 8JBY

  • PubMed Abstract: 

    Tyrosine phosphorylation is an essential post-translational modification that regulates various biological events and is implicated in many diseases including cancer and atherosclerosis. Vascular endothelial protein tyrosine phosphatase (VE-PTP), which plays an important role in vascular homeostasis and angiogenesis, is therefore an attractive drug target for these diseases. However, there are still no drugs targeting PTP including VE-PTP. In this paper, we report the discovery of a novel VE-PTP inhibitor, Cpd-2, by fragment-based screening combining various biophysical techniques. Cpd-2 is the first VE-PTP inhibitor with a weakly acidic structure and high selectivity, unlike known strongly acidic inhibitors. We believe that this compound represents a new possibility for the development of bioavailable VE-PTP inhibitors.


  • Organizational Affiliation

    Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase beta
A, B
295Homo sapiensMutation(s): 0 
Gene Names: PTPRBPTPB
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P23467 (Homo sapiens)
Explore P23467 
Go to UniProtKB:  P23467
PHAROS:  P23467
GTEx:  ENSG00000127329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23467
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.467α = 90
b = 123.467β = 90
c = 178.909γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release