2CMA

Structural Basis for Inhibition of Protein Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Inhibition of Protein-Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics.

Ala, P.J.Gonneville, L.Hillman, M.C.Becker-Pasha, M.Wei, M.Reid, B.G.Klabe, R.Yue, E.W.Wayland, B.Douty, B.Polam, P.Wasserman, Z.Bower, M.Combs, A.P.Burn, T.C.Hollis, G.F.Wynn, R.

(2006) J.Biol.Chem. 281: 32784

  • DOI: 10.1074/jbc.M606873200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The h ...

    Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe(182) of the flap, and the side chain of Arg(221). When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors.


    Organizational Affiliation

    Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA. pauljala@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
A
327Homo sapiensMutation(s): 0 
Gene 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
F20
Query on F20

Download SDF File 
Download CCD File 
A
N-BENZOYL-L-PHENYLALANYL-4-[(5S)-1,1-DIOXIDO-3-OXOISOTHIAZOLIDIN-5-YL]-L-PHENYLALANINAMIDE
ISOTHIAZOLIDINONE ANALOG
C28 H28 N4 O6 S
ZSFPNCCMRAHJSA-HJOGWXRNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F20IC50: 185 nM BINDINGMOAD
F20IC50: 185 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.700α = 90.00
b = 88.220β = 96.83
c = 49.840γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection