8JBY | pdb_00008jby

Vascular endothelial protein tyrosine phosphatase in complex with Cpd-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.207 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8JBY

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 69.26 kDa 
  • Atom Count: 4,958 
  • Modeled Residue Count: 559 
  • Deposited Residue Count: 590 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U7L
(Subject of Investigation/LOI)

Query on U7L



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
4-(hydroxymethyl)-5-(1-methylindol-3-yl)-1,2-oxazole-3-carboxylic acid
C14 H12 N2 O4
JJKVKHLXSDXTKH-UHFFFAOYSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.207 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.692α = 90
b = 123.692β = 90
c = 181.738γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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