1NNY

Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Compound 23 Using a Linked-Fragment Strategy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.218 

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:  
    1NL9, 1NO6, 1NNY

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase, non-receptor type 1A321Homo sapiensMutation(s): 0 
Gene Names: PTPN1 OR PTP1BPTPN1PTP1B
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS  P18031
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
515
Query on 515

Download CCD File 
A
3-({5-[(N-ACETYL-3-{4-[(CARBOXYCARBONYL)(2-CARBOXYPHENYL)AMINO]-1-NAPHTHYL}-L-ALANYL)AMINO]PENTYL}OXY)-2-NAPHTHOIC ACID
C40 H37 N3 O10
URRKGBLRIVECAH-YTTGMZPUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
515Ki:  22   nM  BindingDB
515Ki :  22   nM  PDBBind
515Ki:  20   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.11α = 90
b = 89.11β = 90
c = 106.21γ = 120
Software Package:
Software NamePurpose
CNXrefinement
MAR345data collection
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description