1LQF

Structure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of PTP-1B in complex with a peptide inhibitor reveals an alternative binding mode for bisphosphonates.

Asante-Appiah, E.Patel, S.Dufresne, C.Roy, P.Wang, Q.Patel, V.Friesen, R.W.Ramachandran, C.Becker, J.W.Leblanc, Y.Kennedy, B.P.Scapin, G.

(2002) Biochemistry 41: 9043-9051


  • PubMed Abstract: 
  • Inhibitors of PTP-1B could be therapeutically beneficial in the treatment of type 2 diabetes. Owing to the large number of phosphatases in the cell, inhibitors against PTP-1B must not only be potent but selective as well. N-Benzoyl-L-glutamyl-[4-phos ...

    Inhibitors of PTP-1B could be therapeutically beneficial in the treatment of type 2 diabetes. Owing to the large number of phosphatases in the cell, inhibitors against PTP-1B must not only be potent but selective as well. N-Benzoyl-L-glutamyl-[4-phosphono(difluoromethyl)]-L-phenylalanine-[4-phosphono(difluoro-methyl)]-L-phenylalanineamide (BzN-EJJ-amide) is a low nanomolar inhibitor of PTP-1B that shows selectivity over several protein tyrosine phosphatases. To gain an insight into the basis of its potency and selectivity, we evaluated several analogues of the inhibitor and introduced amino acid substitutions into PTP-1B by site-directed mutagenesis. We also determined the crystal structure of PTP-1B in complex with BzN-EJJ-amide at 2.5 A resolution. Our results indicate that the high inhibitory potency is due to interactions of several of its chemical groups with specific protein residues. An interaction between BzN-EJJ-amide and Asp48 is of particular significance, as substitution of Asp48 to alanine resulted in a 100-fold loss in potency. The crystal structure also revealed an unexpected binding orientation for a bisphosphonate inhibitor on PTP-1B, where the second difluorophosphonomethyl phenylalanine (F(2)PMP) moiety is bound close to Arg47 rather than in the previously identified second aryl phosphate site demarked by Arg24 and Arg254. Our results suggest that potent and selective PTP-1B inhibitors may be designed by targeting the region containing Arg47 and Asp48.


    Related Citations: 
    • The YRD motif is a major determinant of substrate and inhibitor specificity in T-cell protein-tyrosine phosphatase
      Asante-Appiah, E.,Ball, K.,Bateman, K.,Skorey, K.,Friesen, R.,Desponts, C.,Payette, P.,Bayly, C.,Zamboni, R.,Scapin, G.,Ramachandran, C.,Kennedy, B.P.
      (2001) J.Biol.Chem. 276: 26036


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada. Ernest_Asanteappiah@Merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protein-tyrosine phosphatase, non-receptor type 1
A, B, C, D
295Homo 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
BGD
Query on BGD

Download SDF File 
Download CCD File 
A, B, C, D
N-BENZOYL-L-GLUTAMYL-[4-PHOSPHONO(DIFLUOROMETHYL)]-L-PHENYLALANINE-[4-PHOSPHONO(DIFLUORO-METHYL)]-L-PHENYLALANINEAMIDE
4-BENZOYLAMINO-4-{1-{1-CARBAMOYL-2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ETHYLCARBAMOYL}-2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ETHYLCARBAMOYL}-BUTYRIC ACID
C32 H34 F4 N4 O12 P2
UJIWNECQGQOIKP-SDHOMARFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BGDIC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 186.866α = 90.00
b = 154.421β = 94.56
c = 64.598γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MAR345data collection
X-GENdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-24
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description