2B07

Crystal structure of PTP1B with Tricyclic Thiophene inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Bicyclic and tricyclic thiophenes as protein tyrosine phosphatase 1B inhibitors.

Moretto, A.F.Kirincich, S.J.Xu, W.X.Smith, M.J.Wan, Z.K.Wilson, D.P.Follows, B.C.Binnun, E.Joseph-McCarthy, D.Foreman, K.Erbe, D.V.Zhang, Y.L.Tam, S.K.Tam, S.Y.Lee, J.

(2006) Bioorg Med Chem 14: 2162-2177

  • DOI: https://doi.org/10.1016/j.bmc.2005.11.005
  • Primary Citation of Related Structures:  
    2AZR, 2B07

  • PubMed Abstract: 

    A novel pyridothiophene inhibitor of PTP1B was discovered by rational screening of phosphotyrosine mimics at high micromolar concentrations. The potency of this lead compound has been improved significantly by medicinal chemistry guided by X-ray crystallography and molecular modeling. Excellent consistency has been observed between structure-activity relationships and structural information from PTP1B-inhibitor complexes.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase, non-receptor type 1299Homo sapiensMutation(s): 0 
Gene Names: PTPN1PTP1B
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
PHAROS:  P18031
GTEx:  ENSG00000196396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
598
Query on 598

Download Ideal Coordinates CCD File 
B [auth A]6-{[1-(BENZYLSULFONYL)PIPERIDIN-4-YL]AMINO}-3-(CARBOXYMETHOXY)THIENO[3,2-B][1]BENZOTHIOPHENE-2-CARBOXYLIC ACID
C25 H24 N2 O7 S3
UEELPALQXUYKFT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
598 BindingDB:  2B07 Ki: 370 (nM) from 1 assay(s)
PDBBind:  2B07 Ki: 370 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.239α = 90
b = 88.239β = 90
c = 104.063γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations