Crystal structure PTP1B complex with small molecule inhibitor LZP-25

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 

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This is version 1.3 of the entry. See complete history


Targeting inactive enzyme conformation: aryl diketoacid derivatives as a new class of PTP1B inhibitors.

Liu, S.Zeng, L.F.Wu, L.Yu, X.Xue, T.Gunawan, A.M.Long, Y.Q.Zhang, Z.Y.

(2008) J Am Chem Soc 130: 17075-17084

  • DOI: https://doi.org/10.1021/ja8068177
  • Primary Citation of Related Structures:  
    3EAX, 3EB1

  • PubMed Abstract: 

    There has been considerable interest in protein tyrosine phosphatase 1B (PTP1B) as a therapeutic target for diabetes, obesity, as well as cancer. Identifying inhibitory compounds with good bioavailability is a major challenge of drug discovery programs targeted toward PTPs. Most current PTP active site-directed pharmacophores are negatively charged pTyr mimetics which cannot readily enter the cell. This lack of cell permeability limits the utility of such compounds in signaling studies and further therapeutic development. We identify aryl diketoacids as novel pTyr surrogates and show that neutral amide-linked aryl diketoacid dimers also exhibit excellent PTP inhibitory activity. Kinetic studies establish that these aryl diketoacid derivatives act as noncompetitive inhibitors of PTP1B. Crystal structures of ligand-bound PTP1B reveal that both the aryl diketoacid and its dimeric derivative bind PTP1B at the active site, albeit with distinct modes of interaction, in the catalytically inactive, WPD loop open conformation. Furthermore, dimeric aryl diketoacids are cell permeable and enhance insulin signaling in hepatoma cells, suggesting that targeting the inactive conformation may provide a unique opportunity for creating active site-directed PTP1B inhibitors with improved pharmacological properties.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1321Homo sapiensMutation(s): 0 
Gene Names: PTPN1PTP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
GTEx:  ENSG00000196396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LZQ

Download Ideal Coordinates CCD File 
B [auth A]4-[3-(dibenzylamino)phenyl]-2,4-dioxobutanoic acid
C24 H21 N O4
Binding Affinity Annotations 
IDSourceBinding Affinity
LZQ PDBBind:  3EB1 Ki: 1.63e+4 (nM) from 1 assay(s)
BindingDB:  3EB1 IC50: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.526α = 90
b = 88.526β = 90
c = 104.722γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.3: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations