2H03

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

• PDB DOI: https://doi.org/10.2210/pdb2H03/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-13 Released: 2006-06-13 
• Deposition Author(s): Evdokimov, A.G., Pokross, M.E., Walter, R.L., Mekel, M., Gray, J.L., Peters, K.G., Maier, M.B., Amarasinghe, K.D., Clark, C.M., Nichols, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.217 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Starting Model: experimental

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

• PubMed: 16759857 
• 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.

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Organizational Affiliation: 

Procter & Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.39 kDa 
• Atom Count: 2,625 
• Modelled Residue Count: 288 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein tyrosine phosphatase, receptor type, B,	A	291	Homo sapiens	Mutation(s): 2  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UN	F [auth A]	(4-{4-[(TERT-BUTOXYCARBONYL)AMINO]-2,2-BIS(ETHOXYCARBONYL)BUTYL}PHENYL)SULFAMIC ACID C21 H32 N2 O9 S VHLMZWXTBDMYOE-UHFFFAOYSA-N
CL	B [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3UN	PDBBind:  2H03	IC50: 90 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.217 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.316	α = 90
b = 38.934	β = 103.91
c = 66.062	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Evdokimov, A.G., Pokross, M.E., Walter, R.L., Mekel, M., Gray, J.L., Peters, K.G., Maier, M.B., Amarasinghe, K.D., Clark, C.M., Nichols, R.

Revision History  

• 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: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description