1Q6N

THE STRUCTURE OF PHOSPHOTYROSINE PHOSPHATASE 1B IN COMPLEX WITH COMPOUND 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Structural Basis for the Selectivity of Benzotriazole Inhibitors of Ptp1B

Scapin, G.Patel, S.B.Becker, J.W.Wang, Q.Desponts, C.Waddleton, D.Skorey, K.Cromlish, W.Bayly, C.Therien, M.Gauthier, J.Y.Li, C.S.Lau, C.K.Ramachandran, C.Kennedy, B.P.Asante-Appiah, E.

(2003) Biochemistry 42: 11451-11459

  • DOI: 10.1021/bi035098j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein tyrosine phosphatase 1B (PTP1B) has been implicated in the regulation of the insulin signaling pathway and represents an attractive target for the design of inhibitors in the treatment of type 2 diabetes and obesity. Inspection of the structu ...

    Protein tyrosine phosphatase 1B (PTP1B) has been implicated in the regulation of the insulin signaling pathway and represents an attractive target for the design of inhibitors in the treatment of type 2 diabetes and obesity. Inspection of the structure of PTP1B indicates that potent PTP1B inhibitors may be obtained by targeting a secondary aryl phosphate-binding site as well as the catalytic site. We report here the crystal structures of PTP1B in complex with first and second generation aryldifluoromethyl-phosphonic acid inhibitors. While all compounds bind in a previously unexploited binding pocket near the primary binding site, the second generation compounds also reach into the secondary binding site, and exhibit moderate selectivity for PTP1B over the closely related T-cell phosphatase. The molecular basis for the selectivity has been confirmed by single point mutation at position 52, where the two phosphatases differ by a phenylalanine-to-tyrosine switch. These compounds present a novel platform for the development of potent and selective PTP1B inhibitors.


    Organizational Affiliation

    Merck Research Laboratory, P. O. Box 2000, Rahway, New Jersey 07065, USA. giovanna_scapin@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine phosphatase, non-receptor type 1
A, B
310Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
P90
Query on P90

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Download CCD File 
A, B
{4-[(2S,4E)-2-(1,3-BENZOTHIAZOL-2-YL)-2-(1H-1,2,3-BENZOTRIAZOL-1-YL)-5-PHENYLPENT-4-ENYL]PHENYL}(DIFLUORO)METHYLPHOSPHONIC ACID
C31 H25 F2 N4 O3 P S
GBLDYRVJENYQNH-AGLOJYHOSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P90IC50: 23 nM (100) BINDINGDB
P90IC50: 23 nM BINDINGMOAD
P90IC50: 23 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.878α = 90.00
b = 88.409β = 90.00
c = 139.224γ = 90.00
Software Package:
Software NamePurpose
X-GENdata reduction
CNXphasing
X-GENdata scaling
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-30
    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: Refinement description