1Q1M

A Highly Efficient Approach to a Selective and Cell Active PTP1B inhibitors

• PDB DOI: https://doi.org/10.2210/pdb1Q1M/pdb

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


• Deposited: 2003-07-22 Released: 2003-09-16 
• Deposition Author(s): Liu, G., Xin, Z., Pei, Z., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Zhao, H., Lubben, T.H., Ballaron, S.J., Haasch, 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: 2.60 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor.

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

(2003) J Med Chem 46: 4232-4235

• PubMed: 13678400 
• DOI: https://doi.org/10.1021/jm034122o
• Primary Citation of Related Structures:  
  1Q1M


• PubMed Abstract: 
  

  Using an NMR-based fragment screening and X-ray crystal structure-based assembly, starting with millimolar ligands for both the catalytic site and the second phosphotyrosine binding site, we have identified a small-molecule inhibitor of protein tyrosine phosphatase 1B with low micromolar inhibition constant, high selectivity (30-fold) over the highly homologous T-cell protein tyrosine phosphatase, and good cellular activity in COS-7 cells.

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Organizational Affiliation: 

Metabolic Disease Research and Advanced Technology, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 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: 37.78 kDa 
• Atom Count: 2,589 
• 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 OR 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
234	B [auth A]	5-{2-FLUORO-5-[3-(3-HYDROXY-2-METHOXYCARBONYL-PHENOXY)-PROPENYL]-PHENYL}-ISOXAZOLE-3-CARBOXYLIC ACID C21 H16 F N O7 QKHWJUMLYAYZFS-ONEGZZNKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
234	BindingDB:  1Q1M	Ki: min: 6.9, max: 7000 (nM) from 5 assay(s)
		IC50: min: 6900, max: 1.10e+5 (nM) from 2 assay(s)
	PDBBind:  1Q1M	Ki: 6900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.208 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.294	α = 90
b = 88.294	β = 90
c = 104.378	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: 2003-09-16 
Deposition Author(s): Liu, G., Xin, Z., Pei, Z., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Zhao, H., Lubben, T.H., Ballaron, S.J., Haasch, D.L., Kaszubska, W., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

Revision History  

• Version 1.0: 2003-09-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description