1ONZ | pdb_00001onz

Oxalyl-aryl-Amino Benzoic acid Inhibitors of PTP1B, compound 8b

• PDB DOI: https://doi.org/10.2210/pdb1ONZ/pdb

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


• Deposited: 2003-03-02 Released: 2003-05-20 
• Deposition Author(s): Liu, G., Szczepankiewicz, B.G., Pei, Z., Janowich, D.A., Xin, Z., Hadjuk, P.J., Abad-Zapatero, C., Liang, H., Hutchins, C.W., Fesik, S.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Mika, A.K., Zinker, B.A., Trevillyan, J.M., Jirousek, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.223 (Depositor) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Discovery and Structure-Activity Relationship of Oxalylarylaminobenzoic Acids as Inhibitors of Protein Tyrosine Phosphatase 1B

Liu, G., Szczepankiewicz, B.G., Pei, Z., Janowich, D.A., Xin, Z., Hadjuk, P.J., Abad-Zapatero, C., Liang, H., Hutchins, C.W., Fesik, S.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Mika, A.K., Zinker, B.A., Trevillyan, J.M., Jirousek, M.R.

(2003) J Med Chem 46: 2093-2103

• PubMed: 12747781 
• DOI: https://doi.org/10.1021/jm0205696
• Primary Citation Related Structures: 
  1ONY, 1ONZ


• PubMed Abstract: 
  

  Protein Tyrosine phosphatase 1B (PTP1B) has been implicated as a key negative regulator of both insulin and leptin signaling pathways. Using an NMR-based screening approach with 15N- and 13C-labeled PTP1B, we have identified 2,3-dimethylphenyloxalylaminobenzoic acid (1) as a general, reversible, and competitive PTPase inhibitor. Structure-based approach guided by X-ray crystallography facilitated the development of 1 into a novel series of potent and selective PTP1B inhibitors occupying both the catalytic site and a portion of the noncatalytic, second phosphotyrosine binding site. Interestingly, oral biovailability has been observed in rats for some compounds. Furthermore, we demonstrated in vivo plasma glucose lowering effects with compound 12d in ob/ob mice.

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Organizational Affiliation: 
• Metabolic Disease Research and Advanced Technology, Global Pharmaceutical Research and Development, Abbott Laboratories, 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: 37.72 kDa 
• Atom Count: 2,606 
• Modeled Residue Count: 283 
• 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
968	B [auth A]	2-[(7-HYDROXY-NAPHTHALEN-1-YL)-OXALYL-AMINO]-BENZOIC ACID C19 H13 N O6 IGOULVZYQKJJKC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
968	BindingDB:  1ONZ	Ki: min: 1.70e+4, max: 2.51e+4 (nM) from 2 assay(s)
		Kd: 8000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.223 (Depositor) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.614	α = 90
b = 88.614	β = 90
c = 105.167	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: 2003-05-20 
Deposition Author(s): Liu, G., Szczepankiewicz, B.G., Pei, Z., Janowich, D.A., Xin, Z., Hadjuk, P.J., Abad-Zapatero, C., Liang, H., Hutchins, C.W., Fesik, S.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Mika, A.K., Zinker, B.A., Trevillyan, J.M., Jirousek, M.R.

Revision History  

• Version 1.0: 2003-05-20
  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