3QCG

Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 3-[(3-bromo-4-chlorobenzyl)sulfanyl]thiophene-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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, 3QCE, 3QCF, 3QCH, 3QCI, 3QCJ, 3QCK, 3QCL, 3QCM, 3QCN

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase gamma
A
310Homo sapiensGene Names: PTPRG (PTPG)
EC: 3.1.3.48
Find proteins for P23470 (Homo sapiens)
Go to Gene View: PTPRG
Go to UniProtKB:  P23470
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NX1
Query on NX1

Download SDF File 
Download CCD File 
A
3-[(3-bromo-4-chlorobenzyl)sulfanyl]thiophene-2-carboxylic acid
C12 H8 Br Cl O2 S2
IRIFYVKSSQVSCC-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.500α = 90.00
b = 75.500β = 90.00
c = 152.100γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data reduction
CNXrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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