2H02

Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Design and synthesis of potent, non-peptidic inhibitors of HPTPbeta.

Amarasinghe, K.K., Evdokimov, A.G., Xu, K., Clark, C.M., Maier, M.B., Srivastava, A., Colson, A.O., Gerwe, G.S., Stake, G.E., Howard, B.W., Pokross, M.E., Gray, J.L., Peters, K.G.

(2006) Bioorg Med Chem Lett 16: 4252-4256

  • DOI: https://doi.org/10.1016/j.bmcl.2006.05.074
  • Primary Citation of Related Structures:  
    2H02, 2H03, 2H04

  • PubMed Abstract: 

    The sulfamic acid phosphotyrosine mimetic was coupled with a previously known malonate template to obtain highly selective and potent inhibitors of HPTPbeta. Potentially hydrolyzable malonate ester functionalities were replaced with 1,2,4-oxadiazoles without a significant effect on HPTPbeta potency.

    • Organizational Affiliation: 

    Procter & Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA. Amarasinghe.kk@pg.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein tyrosine phosphatase, receptor type, B,
A, B
313Homo sapiensMutation(s): 0 
Gene Names: PTPRB
EC: 3.1.3.48
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2UN
Query on 2UN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		{4-[2-BENZYL-3-METHOXY-2-(METHOXYCARBONYL)-3-OXOPROPYL]PHENYL}SULFAMIC ACID
C19 H21 N O7 S
SUACYXRSGYYBGT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2UN Binding MOAD:  2H02 IC50: 320 (nM) from 1 assay(s)
PDBBind:  2H02 IC50: 320 (nM) from 1 assay(s)
BindingDB:  2H02 IC50: 320 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.144α = 90
b = 71.724β = 93.41
c = 70.297γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    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: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description