2NTA | pdb_00002nta

Crystal Structure of PTP1B-inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.247 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2NTA

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.bmcl.2007.02.043
  • Primary Citation Related Structures: 
    2NT7, 2NTA

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 35.15 kDa 
  • Atom Count: 2,663 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
521

Query on 521



Download:Ideal Coordinates CCD File
B [auth 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.247 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.256α = 90
b = 88.256β = 90
c = 104.17γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-17
    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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations