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

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This is version 1.4 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:  
    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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase, non-receptor type 1A298Homo sapiensMutation(s): 3 
Gene Names: PTPN1, PTP1B
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FG1
Query on FG1
Download Ideal Coordinates CCD File 
B [auth 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: 3.10 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
REFMACrefinement
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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