1NZ7

POTENT, SELECTIVE INHIBITORS OF PROTEIN TYROSINE PHOSPHATASE 1B USING A SECOND PHOSPHOTYROSINE BINDING SITE, complexed with compound 19.

• PDB DOI: https://doi.org/10.2210/pdb1NZ7/pdb

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


• Deposited: 2003-02-16 Released: 2003-05-20 
• Deposition Author(s): Xin, Z., Oost, T.K., Abad-Zapatero, C., Hajduk, P.J., Pei, Z., Szczepankiewicz, B.G., Hutchins, C.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Trevillyan, J.M., Jirousek, M.R., Liu, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Potent, Selective Inhibitors of Protein Tyrosine Phosphatase 1B

Xin, Z., Oost, T.K., Abad-Zapatero, C., Hajduk, P.J., Pei, Z., Szczepankiewicz, B.G., Hutchins, C.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Trevillyan, J.M., Jirousek, M.R., Liu, G.

(2003) Bioorg Med Chem Lett 13: 1887-1890

• PubMed: 12749891 
• DOI: https://doi.org/10.1016/s0960-894x(03)00302-0
• Primary Citation of Related Structures:  
  1NZ7


• PubMed Abstract: 
  

  We have previously reported a novel series of oxalyl-aryl-amino benzoic acid-based, catalytic site-directed, competitive, reversible protein tyrosine phosphatase 1B (PTP1B) inhibitors. With readily access to key intermediates, we utilized a solution phase parallel synthesis approach and rapidly identified a highly potent PTP1B inhibitor (19, K(i)=76 nM) with moderate selectivity (5-fold) over T-cell PTPase (TCPTP) through interacting with a second phosphotyrosine binding site (site 2) in the close proximity to the catalytic site.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.04 kDa 
• Atom Count: 2,563 
• Modelled 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
GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
901	B [auth A]	2-[(4-{2-ACETYLAMINO-2-[4-(1-CARBOXY-3-METHYLSULFANYL-PROPYLCARBAMOYL)-BUTYLCARBAMOYL]-ETHYL}-2-ETHYL-PHENYL)-OXALYL-AM INO]-BENZOIC ACID C32 H40 N4 O10 S JYWLVKREVMTEJA-ZEQRLZLVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
901	BindingDB:  1NZ7	Ki: min: 63, max: 77 (nM) from 3 assay(s)
	PDBBind:  1NZ7	Ki: 76 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.194 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.84	α = 90
b = 88.84	β = 90
c = 105.435	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-20 
Deposition Author(s): Xin, Z., Oost, T.K., Abad-Zapatero, C., Hajduk, P.J., Pei, Z., Szczepankiewicz, B.G., Hutchins, C.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Trevillyan, J.M., Jirousek, M.R., Liu, G.

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, Structure summary