1G7F

HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH PNU177496


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Small molecule peptidomimetics containing a novel phosphotyrosine bioisostere inhibit protein tyrosine phosphatase 1B and augment insulin action.

Bleasdale, J.E.Ogg, D.Palazuk, B.J.Jacob, C.S.Swanson, M.L.Wang, X.Y.Thompson, D.P.Conradi, R.A.Mathews, W.R.Laborde, A.L.Stuchly, C.W.Heijbel, A.Bergdahl, K.Bannow, C.A.Smith, C.W.Svensson, C.Liljebris, C.Schostarez, H.J.May, P.D.Stevens, F.C.Larsen, S.D.

(2001) Biochemistry 40: 5642-5654

  • DOI: 10.1021/bi002865v
  • Primary Citation of Related Structures:  
    1G7F, 1G7G

  • PubMed Abstract: 
  • Protein tyrosine phosphatase 1B (PTP1B) attenuates insulin signaling by catalyzing dephosphorylation of insulin receptors (IR) and is an attractive target of potential new drugs for treating the insulin resistance that is central to type II diabetes. Several analogues of cholecystokinin(26)(-)(33) (CCK-8) were found to be surprisingly potent inhibitors of PTP1B, and a common N-terminal tripeptide, N-acetyl-Asp-Tyr(SO(3)H)-Nle-, was shown to be necessary and sufficient for inhibition ...

    Protein tyrosine phosphatase 1B (PTP1B) attenuates insulin signaling by catalyzing dephosphorylation of insulin receptors (IR) and is an attractive target of potential new drugs for treating the insulin resistance that is central to type II diabetes. Several analogues of cholecystokinin(26)(-)(33) (CCK-8) were found to be surprisingly potent inhibitors of PTP1B, and a common N-terminal tripeptide, N-acetyl-Asp-Tyr(SO(3)H)-Nle-, was shown to be necessary and sufficient for inhibition. This tripeptide was modified to reduce size and peptide character, and to replace the metabolically unstable sulfotyrosyl group. This led to the discovery of a novel phosphotyrosine bioisostere, 2-carboxymethoxybenzoic acid, and to analogues that were >100-fold more potent than the CCK-8 analogues and >10-fold selective for PTP1B over two other PTP enzymes (LAR and SHP-2), a dual specificity phosphatase (cdc25b), and a serine/threonine phosphatase (calcineurin). These inhibitors disrupted the binding of PTP1B to activated IR in vitro and prevented the loss of tyrosine kinase (IRTK) activity that accompanied PTP1B-catalyzed dephosphorylation of IR. Introduction of these poorly cell permeant inhibitors into insulin-treated cells by microinjection (oocytes) or by esterification to more lipophilic proinhibitors (3T3-L1 adipocytes and L6 myocytes) resulted in increased potency, but not efficacy, of insulin. In some instances, PTP1B inhibitors were insulin-mimetic, suggesting that in unstimulated cells PTP1B may suppress basal IRTK activity. X-ray crystallography of PTP1B-inhibitor complexes revealed that binding of an inhibitor incorporating phenyl-O-malonic acid as a phosphotyrosine bioisostere occurred with the mobile WPD loop in the open conformation, while a closely related inhibitor with a 2-carboxymethoxybenzoic acid bioisostere bound with the WPD loop closed, perhaps accounting for its superior potency. These CCK-derived peptidomimetic inhibitors of PTP1B represent a novel template for further development of potent, selective inhibitors, and their cell activity further justifies the selection of PTP1B as a therapeutic target.


    Organizational Affiliation

    Research and Development, Pharmacia Corporation, Kalamazoo, Michigan 49007, USA. John.E.Bleasdale@am.pnu.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1A298Homo sapiensMutation(s): 0 
Gene Names: PTPN1PTP1B
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
PHAROS:  P18031
GTEx:  ENSG00000196396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INZ
Query on INZ

Download Ideal Coordinates CCD File 
B [auth A]2-{4-[(2S)-2-[({[(1S)-1-CARBOXY-2-PHENYLETHYL]AMINO}CARBONYL)AMINO]-3-OXO-3-(PENTYLAMINO)PROPYL]PHENOXY}MALONIC ACID
C27 H33 N3 O9
BKONADSQADEJJP-SFTDATJTSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
INZ BindingDB:  1G7F Ki: 3400 (nM) from 1 assay(s)
Binding MOAD:  1G7F Ki: 3400 (nM) from 1 assay(s)
PDBBind:  1G7F Ki: 3400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.74α = 90
b = 83.82β = 90
c = 88.66γ = 90
Software Package:
Software NamePurpose
MERLOTphasing
REFMACrefinement
SMARTdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance