1L8G

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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


  • 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 Asp ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
A
321Homo 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
DBD
Query on DBD

Download SDF File 
Download CCD File 
A
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
C18 H14 N2 O9 S2
MDYIGSPVMWSFEZ-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DBDKi: 1100 nM (99) BINDINGDB
DBDKi: 600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.258α = 90.00
b = 88.258β = 90.00
c = 103.617γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance