3QCJ

Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 5-[({3-[(3,4-dichlorobenzyl)sulfanyl]thiophen-2-yl}carbonyl)sulfamoyl]-2-methoxybenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report



Literature

Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop

Sheriff, S.Beno, B.R.Zhai, W.Kostich, W.A.McDonnell, P.A.Kish, K.Goldfarb, V.Gao, M.Kiefer, S.E.Yanchunas, J.Huang, Y.Shi, S.Zhu, S.Dzierba, C.Bronson, J.Macor, J.E.Appiah, K.K.Westphal, R.S.O'Connell, J.Gerritz, S.W.

(2011) J Med Chem 54: 6548-6562

  • DOI: 10.1021/jm2003766
  • Primary Citation of Related Structures:  
    3QCB, 3QCC, 3QCD, 3QCM, 3QCN, 3QCE, 3QCF, 3QCG, 3QCH, 3QCI

  • PubMed Abstract: 
  • Protein tyrosine phosphatases (PTPs) catalyze the dephosphorylation of tyrosine residues, a process that involves a conserved tryptophan-proline-aspartate (WPD) loop in catalysis. In previously determined structures of PTPs, the WPD-loop has been obs ...

    Protein tyrosine phosphatases (PTPs) catalyze the dephosphorylation of tyrosine residues, a process that involves a conserved tryptophan-proline-aspartate (WPD) loop in catalysis. In previously determined structures of PTPs, the WPD-loop has been observed in either an "open" conformation or a "closed" conformation. In the current work, X-ray structures of the catalytic domain of receptor-like protein tyrosine phosphatase γ (RPTPγ) revealed a ligand-induced "superopen" conformation not previously reported for PTPs. In the superopen conformation, the ligand acts as an apparent competitive inhibitor and binds in a small hydrophobic pocket adjacent to, but distinct from, the active site. In the open and closed WPD-loop conformations of RPTPγ, the side chain of Trp1026 partially occupies this pocket. In the superopen conformation, Trp1026 is displaced allowing a 3,4-dichlorobenzyl substituent to occupy this site. The bound ligand prevents closure of the WPD-loop over the active site and disrupts the catalytic cycle of the enzyme.


    Related Citations: 
    • Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms
      Kish, K., McDonnell, P.A., Goldfarb, V., Gao, M., Metzler, W.J., Langley, D.R., Bryson, J.W., Kiefer, S.E., Kostich, W.A., Carpenter, B., Westphal, R.S., Sheriff, S.
      () To be published --: --

    Organizational Affiliation

    Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States. steven.sheriff@bms.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase gammaA310Homo sapiensMutation(s): 0 
Gene Names: PTPGPTPRG
EC: 3.1.3.48
Find proteins for P23470 (Homo sapiens)
Explore P23470 
Go to UniProtKB:  P23470
NIH Common Fund Data Resources
PHAROS  P23470
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NX4
Query on NX4

Download CCD File 
A
5-[({3-[(3,4-dichlorobenzyl)sulfanyl]thiophen-2-yl}carbonyl)sulfamoyl]-2-methoxybenzoic acid
C20 H15 Cl2 N O6 S3
HBYORZQNJPQOQI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NX4IC50 :  500   nM  PDBBind
NX4IC50:  500   nM  Binding MOAD
NX4IC50:  500   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.7α = 90
b = 75.7β = 90
c = 152.2γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-01-16 
  • Released Date: 2011-12-28 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release