1PH0

Non-carboxylic Acid-Containing Inhibitor of PTP1B Targeting the Second Phosphotyrosine Site

• PDB DOI:  https://doi.org/10.2210/pdb1PH0/pdb

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


• Deposited: 2003-05-29 Released: 2003-07-29 
• Deposition Author(s): Liu, G., Xin, Z., Liang, H., Abad-Zapatero, C., Hajduk, P., Janowick, D., Szczepankiewicz, B., Pei, Z., Hutchins, C.W., Ballaron, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.192 
• R-Value Observed: 0.213 

Literature

Selective Protein Tyrosine Phosphatase 1B Inhibitors: Targeting the Second Phosphotyrosine Binding Site with Non-Carboxylic Acid-Containing Ligands.

Liu, G., Xin, Z., Liang, H., Abad-Zapatero, C., Hajduk, P.J., Janowick, D.A., Szczepankiewicz, B.G., Pei, Z., Hutchins, C.W., Ballaron, S.J., Stashko, M.A., Lubben, T.H., Berg, C.E., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

(2003) J Med Chem 46: 3437-3440

• PubMed: 12877578 
• DOI: https://doi.org/10.1021/jm034088d
• Primary Citation of Related Structures:  
  1PH0


• PubMed Abstract: 
  

Protein tyrosine phosphatase (PTPase) 1B (PTP1B) has been implicated as a key negative regulator of both insulin and leptin signaling cascades. We identified several salicylic acid-based ligands for the second phosphotyrosine binding site of PTP1B using a NMR-based screening. Structure-based linking with a catalytic site-directed oxalylarylaminobenzoic acid-based pharmacophore led to the identification of a novel series of potent PTP1B inhibitors exhibiting 6-fold selectivity over the highly homologous T-cell PTPase (TCPTP) and high selectivity over other phosphatases.

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Organizational Affiliation: 

Metabolic Disease Research and Advanced Technology, 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: 38.04 kDa 
• Atom Count: 2,560 
• 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, 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
418	B [auth A]	2-{4-[2-(S)-ALLYLOXYCARBONYLAMINO-3-{4-[(2-CARBOXY-PHENYL)-OXALYL-AMINO]-PHENYL}-PROPIONYLAMINO]-BUTOXY}-6-HYDROXY-BENZ OIC ACID METHYL ESTER C34 H35 N3 O12 JTJBRKLISQICDU-DEOSSOPVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
418	BindingDB:  1PH0	Ki: min: 120, max: 126 (nM) from 2 assay(s)
	PDBBind:  1PH0	Ki: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.192 
• R-Value Observed: 0.213 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.94	α = 90
b = 88.94	β = 90
c = 105.363	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: 2003-07-29 
Deposition Author(s): Liu, G., Xin, Z., Liang, H., Abad-Zapatero, C., Hajduk, P., Janowick, D., Szczepankiewicz, B., Pei, Z., Hutchins, C.W., Ballaron, S.J.

Revision History  

• Version 1.0: 2003-07-29
  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