1NWE

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1021/ja034440c
  • Primary Citation of Related Structures:  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 rem ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine phosphatase, non-receptor type 1
A
298Homo sapiensGene Names: PTPN1 (PTP1B)
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Go to Gene View: PTPN1
Go to UniProtKB:  P18031
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FG1
Query on FG1

Download SDF File 
Download CCD File 
A
N-[4-(2-{2-[3-(2-BROMO-ACETYLAMINO)-PROPIONYLAMINO]-3-HYDROXY-PROPIONYLAMINO}-ETHYL)-PHENYL]-OXALAMIC ACID
C18 H23 Br N4 O7
IYAWTDCWUJJPHZ-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.283 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.052α = 90.00
b = 88.052β = 90.00
c = 117.594γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description