Crystal structure of PTP1B complexed with 7-(1,1-Dioxo-1H-benzo[d]isothiazol-3-yloxymethyl)-2-(oxalyl-amino)-4,7-dihydro-5H-thieno[2,3-c]pyran-3-carboxylic acid

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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Steric hindrance as a basis for structure-based design of selective inhibitors of protein-tyrosine phosphatases.

Iversen, L.F.Andersen, H.S.Moller, K.B.Olsen, O.H.Peters, G.H.Branner, S.Mortensen, S.B.Hansen, T.K.Lau, J.Ge, Y.Holsworth, D.D.Newman, M.J.Hundahl Moller, N.P.

(2001) Biochemistry 40: 14812-14820

  • DOI: https://doi.org/10.1021/bi011389l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Utilizing structure-based design, we have previously demonstrated that it is possible to obtain selective inhibitors of protein-tyrosine phosphatase 1B (PTP1B). A basic nitrogen was introduced into a general PTP inhibitor to form a salt bridge to Asp48 in PTP1B and simultaneously cause repulsion in PTPs containing an asparagine in the equivalent position [Iversen, L. F., et al. (2000) J. Biol. Chem. 275, 10300-10307]. Further, we have recently demonstrated that Gly259 in PTP1B forms the bottom of a gateway that allows easy access to the active site for a broad range of substrates, while bulky residues in the same position in other PTPs cause steric hindrance and reduced substrate recognition capacity [Peters, G. H., et al. (2000) J. Biol. Chem. 275, 18201-18209]. The current study was undertaken to investigate the feasibility of structure-based design, utilizing these differences in accessibility to the active site among various PTPs. We show that a general, low-molecular weight PTP inhibitor can be developed into a highly selective inhibitor for PTP1B and TC-PTP by introducing a substituent, which is designed to address the region around residues 258 and 259. Detailed enzyme kinetic analysis with a set of wild-type and mutant PTPs, X-ray protein crystallography, and molecular modeling studies confirmed that selectivity for PTP1B and TC-PTP was achieved due to steric hindrance imposed by bulky position 259 residues in other PTPs.

  • Organizational Affiliation

    Protein Chemistry and Signal Transduction, Novo Nordisk, DK-2880 Bagsvaerd, Denmark. lfiv@novonordisk.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  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 DBD

Download Ideal Coordinates CCD File 
C18 H14 N2 O9 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
DBD PDBBind:  1L8G Ki: 600 (nM) from 1 assay(s)
BindingDB:  1L8G Ki: 1100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.258α = 90
b = 88.258β = 90
c = 103.617γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    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