1NL9

Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Compound 12 Using a Linked-Fragment Strategy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy

Szczepankiewicz, B.G.Liu, G.Hajduk, P.J.Abad-Zapatero, C.Pei, Z.Xin, Z.Lubben, T.Trevillyan, J.M.Stashko, M.A.Ballaron, S.J.Liang, H.Huang, F.Hutchins, C.W.Fesik, S.W.Jirousek, M.R.

(2003) J.Am.Chem.Soc. 125: 4087-4096

  • DOI: 10.1021/ja0296733
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein tyrosine phosphatase 1B (PTP1B) is an enzyme that downregulates the insulin receptor. Inhibition of PTP1B is expected to improve insulin action, and the design of small molecule PTP1B inhibitors to treat type II diabetes has received consider ...

    Protein tyrosine phosphatase 1B (PTP1B) is an enzyme that downregulates the insulin receptor. Inhibition of PTP1B is expected to improve insulin action, and the design of small molecule PTP1B inhibitors to treat type II diabetes has received considerable attention. In this work, NMR-based screening identified a nonselective competitive inhibitor of PTP1B. A second site ligand was also identified by NMR-based screening and then linked to the catalytic site ligand by rational design. X-ray data confirmed that the inhibitor bound with the catalytic site in the native, "open" conformation. The final compound displayed excellent potency and good selectivity over many other phosphatases. The modular approach to drug design described in this work should be applicable for the design of potent and selective inhibitors of other therapeutically relevant protein tyrosine phosphatases.


    Organizational Affiliation

    Metabolic Disease Research, Global Pharmaceutical Research and Development Organization, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA. bruce.szczepankiewicz@abbott.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
989
Query on 989

Download SDF File 
Download CCD File 
A
2-{[4-(2-ACETYLAMINO-2-PENTYLCARBAMOYL-ETHYL)-NAPHTHALEN-1-YL]-OXALYL-AMINO}-BENZOIC ACID
COMPOUND 12, N-ACETYL-4-[(CARBOXYCARBONYL)(2-CARBOXYPHENYL)AMINO]-N-PENTYL-1-NAPTHYLALANIAMIDE
C29 H31 N3 O7
UESXELNYBIOROE-QHCPKHFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
989Ki: 631 - 1100 nM (100) BINDINGDB
989Ki: 1100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.730α = 90.00
b = 88.730β = 90.00
c = 105.910γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
CNXphasing
CNXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    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