3QCM

Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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, 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 observed in either an "open" conformation or a "closed" conformation ...

    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 gamma A, B310Homo sapiensMutation(s): 2 
Gene Names: PTPG, PTPRG
EC: 3.1.3.48
Find proteins for P23470 (Homo sapiens)
Explore P23470 
Go to UniProtKB:  P23470
NIH Common Fund Data Resources
PHAROS:  P23470
GTEx:  ENSG00000144724
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXW
Query on NXW
Download Ideal Coordinates CCD File 
A, B
2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid
C27 H25 Cl2 N3 O3 S
ZFBIDSCNZFTQMQ-UHFFFAOYSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.6α = 90
b = 74.6β = 98.3
c = 81.9γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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