Ptp1B R47C Modified at C47 with N-[4-(2-{2-[3-(2-Bromo-acetylamino)-propionylamino]-3-hydroxy-propionylamino}-ethyl)-phenyl]-oxalamic acid

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.284 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Discovery of a New Phosphotyrosine Mimetic for PTP1B Using Breakaway Tethering

Erlanson, D.A.McDowell, R.S.He, M.M.Randal, M.Simmons, R.L.Kung, J.Waight, A.Hansen, S.K.

(2003) J Am Chem Soc 125: 5602-5603

  • DOI: https://doi.org/10.1021/ja034440c
  • Primary Citation of Related Structures:  
    1NWE, 1NWL

  • PubMed Abstract: 

    Protein tyrosine phosphatases play important roles in many signaling cascades involved in human disease. The identification of druglike inhibitors for these targets is a major challenge, and the discovery of suitable phosphotyrosine (pY) mimetics remains one of the key difficulties. Here we describe an extension of tethering technology, "breakaway tethering", which is ideally suited for discovering such new chemical entities. The approach involves first irreversibly modifying a protein with an extender that contains both a masked thiol and a known pY mimetic. The extender is then cleaved to release the pY mimetic, unmasking the thiol. The resulting protein is screened against a library of disulfide-containing small molecule fragments; any molecules with inherent affinity for the pY binding site will preferentially form disulfides with the extender, allowing for their identification by mass spectrometry. The ability to start from a known substrate mimimizes perturbation of protein structure and increases the opportunity to probe the active site using tethering. We applied this approach to the anti-diabetic protein PTP1B to discover a pY mimetic which belongs to a new molecular class and which binds in a novel fashion.

  • Organizational Affiliation

    Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080, USA. erlanson@sunesis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase, non-receptor type 1298Homo sapiensMutation(s): 3 
Gene Names: PTPN1PTP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
PHAROS:  P18031
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 FG1

Download Ideal Coordinates CCD File 
C18 H23 Br N4 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.284 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.052α = 90
b = 88.052β = 90
c = 117.594γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-06
    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: Advisory, Refinement description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations