Engineering the PTPbeta catalytic domain with improved crystallization properties

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.

Evdokimov, A.G.Pokross, M.Walter, R.Mekel, M.Cox, B.Li, C.Bechard, R.Genbauffe, F.Andrews, R.Diven, C.Howard, B.Rastogi, V.Gray, J.Maier, M.Peters, K.G.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1435-1445

  • DOI: https://doi.org/10.1107/S0907444906037784
  • Primary Citation of Related Structures:  
    2HC1, 2HC2, 2I3R, 2I3U, 2I4E, 2I4G, 2I4H, 2I5X

  • PubMed Abstract: 

    Protein tyrosine phosphatases (PTPs) play roles in many biological processes and are considered to be important targets for drug discovery. As inhibitor development has proven challenging, crystal structure-based design will be very helpful to advance inhibitor potency and selectivity. Successful application of protein crystallography to drug discovery heavily relies on high-quality crystal structures of the protein of interest complexed with pharmaceutically interesting ligands. It is very important to be able to produce protein-ligand crystals rapidly and reproducibly for as many ligands as necessary. This study details our efforts to engineer the catalytic domain of human protein tyrosine phosphatase beta (HPTPbeta-CD) with properties suitable for rapid-turnaround crystallography. Structures of apo HPTPbeta-CD and its complexes with several novel small-molecule inhibitors are presented here for the first time.

  • Organizational Affiliation

    Structural Biology, Procter and Gamble Pharmaceuticals, 8700 Mason-Montgomery Road, Mason, OH 45140, USA. artem@xtals.org

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase beta
A, B
313Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P23467 (Homo sapiens)
Explore P23467 
Go to UniProtKB:  P23467
PHAROS:  P23467
GTEx:  ENSG00000127329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23467
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.973α = 90
b = 71.308β = 93.4
c = 69.69γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description