2NTA

Crystal Structure of PTP1B-inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing acid replacements of thiophene PTP1B inhibitors.

Wan, Z.K.Follows, B.Kirincich, S.Wilson, D.Binnun, E.Xu, W.Joseph-McCarthy, D.Wu, J.Smith, M.Zhang, Y.L.Tam, M.Erbe, D.Tam, S.Saiah, E.Lee, J.

(2007) Bioorg.Med.Chem.Lett. 17: 2913-2920

  • DOI: 10.1016/j.bmcl.2007.02.043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The following account describes our systematic effort to replace one of the carboxylate groups of our diacid thiophene PTP1B inhibitors. Active hits were validated using enzymatic assays before pursuing efforts to improve the potency. Only when the C ...

    The following account describes our systematic effort to replace one of the carboxylate groups of our diacid thiophene PTP1B inhibitors. Active hits were validated using enzymatic assays before pursuing efforts to improve the potency. Only when the C2 carboxylic acid was replaced with another ionizable functional group was reversible and competitive inhibition retained. Use of a tetrazole ring or 1,2,5-thiadiazolidine-3-one-1,1-dioxide as a carboxylate mimetic led to the discovery of two unique starting series that showed improved permeability (PAMPA) and potency of the order of 300nM. The SAR from these efforts underscores some of the major challenges in developing small molecule inhibitors for PTP1B.


    Organizational Affiliation

    Chemical and Screening Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 1
A
299Homo sapiensMutation(s): 0 
Gene Names: PTPN1 (PTP1B)
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Go to Gene View: PTPN1
Go to UniProtKB:  P18031
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
521
Query on 521

Download SDF File 
Download CCD File 
A
5-(4-CHLORO-5-PHENYL-3-THIENYL)-1,2,5-THIADIAZOLIDIN-3-ONE 1,1-DIOXIDE
C12 H9 Cl N2 O3 S2
LCPRWBWCEGWNKF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
521Ki: 16000 nM BINDINGMOAD
521Ki: 16000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.256α = 90.00
b = 88.256β = 90.00
c = 104.170γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
HKL-2000data scaling
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-07 
  • Released Date: 2007-04-17 
  • Deposition Author(s): Xu, W., Follows, B.

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance