A Highly Efficient Approach to a Selective and Cell Active PTP1B inhibitors

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor.

Liu, G.Xin, Z.Pei, Z.Hajduk, P.J.Abad-Zapatero, C.Hutchins, C.W.Zhao, H.Lubben, T.H.Ballaron, S.J.Haasch, D.L.Kaszubska, W.Rondinone, C.M.Trevillyan, J.M.Jirousek, M.R.

(2003) J Med Chem 46: 4232-4235

  • DOI: https://doi.org/10.1021/jm034122o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Using an NMR-based fragment screening and X-ray crystal structure-based assembly, starting with millimolar ligands for both the catalytic site and the second phosphotyrosine binding site, we have identified a small-molecule inhibitor of protein tyrosine phosphatase 1B with low micromolar inhibition constant, high selectivity (30-fold) over the highly homologous T-cell protein tyrosine phosphatase, and good cellular activity in COS-7 cells.

  • Organizational Affiliation

    Metabolic Disease Research and Advanced Technology, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-6098, USA. gaang.liu@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase, non-receptor type 1321Homo sapiensMutation(s): 0 
Gene Names: PTPN1 OR PTP1B
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 234

Download Ideal Coordinates CCD File 
C21 H16 F N O7
Binding Affinity Annotations 
IDSourceBinding Affinity
234 BindingDB:  1Q1M Ki: min: 6310, max: 7000 (nM) from 4 assay(s)
IC50: min: 6900, max: 1.10e+5 (nM) from 2 assay(s)
PDBBind:  1Q1M Ki: 6900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.294α = 90
b = 88.294β = 90
c = 104.378γ = 120
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description