1XBO | pdb_00001xbo

PTP1B complexed with Isoxazole Carboxylic Acid

• PDB DOI: https://doi.org/10.2210/pdb1XBO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-31 Released: 2004-10-19 
• Deposition Author(s): Zhao, H., Liu, G., Xin, Z., Serby, M., Pei, Z., Szczepankiewicz, B.G., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Lubben, T.H., Ballaron, S.J., Hassach, D.L., Kaszubska, W., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.219 (Depositor) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Isoxazole carboxylic acids as protein tyrosine phosphatase 1B (PTP1B) inhibitors.

Zhao, H., Liu, G., Xin, Z., Serby, M.D., Pei, Z., Szczepankiewicz, B.G., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Lubben, T.H., Ballaron, S.J., Haasch, D.L., Kaszubska, W., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

(2004) Bioorg Med Chem Lett 14: 5543-5546

• PubMed: 15482920 
• DOI: https://doi.org/10.1016/j.bmcl.2004.08.063
• Primary Citation of Related Structures:  
  1XBO


• PubMed Abstract: 
  

  Guided by X-ray crystallography, we have extended the structure-activity relationship (SAR) study on an isoxazole carboxylic acid-based PTP1B inhibitor (1) and more potent and equally selective (>20-fold selectivity over the highly homologous T-cell PTPase, TCPTP) PTP1B inhibitors were identified. Inhibitor 7 demonstrated good cellular activity against PTP1B in COS 7 cells.

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Organizational Affiliation: 

Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064-6098, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.79 kDa 
• Atom Count: 2,609 
• Modelled Residue Count: 299 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine phosphatase, non-receptor type 1	A	321	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1, PTP1B EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
PHAROS:  P18031 GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IX1	B [auth A]	5-(3-{3-[3-HYDROXY-2-(METHOXYCARBONYL)PHENOXY]PROPENYL}PHENYL)-4-(HYDROXYMETHYL)ISOXAZOLE-3-CARBOXYLIC ACID C22 H19 N O8 DQSRCEFDWMQCCV-GQCTYLIASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IX1	BindingDB:  1XBO	Ki: min: 0.92, max: 920 (nM) from 2 assay(s)
		IC50: 920 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.219 (Depositor) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.44	α = 90
b = 88.44	β = 90
c = 104.47	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MAR345	data collection
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-19 
Deposition Author(s): Zhao, H., Liu, G., Xin, Z., Serby, M., Pei, Z., Szczepankiewicz, B.G., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Lubben, T.H., Ballaron, S.J., Hassach, D.L., Kaszubska, W., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

Revision History  

• Version 1.0: 2004-10-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description