1NL9

Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Compound 12 Using a Linked-Fragment Strategy

• PDB DOI:  https://doi.org/10.2210/pdb1NL9/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-06 Released: 2003-04-08 
• Deposition Author(s): Szczepankiewicz, B.G., Liu, G., Hajduk, P.J., Abad-Zapatero, C., Pei, Z., Xin, Z., Lubben, T., Trevillyan, J.M., Stashko, M.A., Ballaron, S.J., Liang, H., Huang, F., Hutchins, C.W., Fesik, S.W., Jirousek, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.192 
• R-Value Observed: 0.208 

Literature

Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy

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

(2003) J Am Chem Soc 125: 4087-4096

• PubMed: 12670229 
• DOI: https://doi.org/10.1021/ja0296733
• Primary Citation of Related Structures:  
  1NL9, 1NNY, 1NO6


• PubMed Abstract: 
  

Protein tyrosine phosphatase 1B (PTP1B) is an enzyme that downregulates the insulin receptor. Inhibition of PTP1B is expected to improve insulin action, and the design of small molecule PTP1B inhibitors to treat type II diabetes has received considerable attention. In this work, NMR-based screening identified a nonselective competitive inhibitor of PTP1B. A second site ligand was also identified by NMR-based screening and then linked to the catalytic site ligand by rational design. X-ray data confirmed that the inhibitor bound with the catalytic site in the native, "open" conformation. The final compound displayed excellent potency and good selectivity over many other phosphatases. The modular approach to drug design described in this work should be applicable for the design of potent and selective inhibitors of other therapeutically relevant protein tyrosine phosphatases.

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Organizational Affiliation: 

Metabolic Disease Research, Global Pharmaceutical Research and Development Organization, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, 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: 37.9 kDa 
• Atom Count: 2,625 
• 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
989	B [auth A]	2-{[4-(2-ACETYLAMINO-2-PENTYLCARBAMOYL-ETHYL)-NAPHTHALEN-1-YL]-OXALYL-AMINO}-BENZOIC ACID C29 H31 N3 O7 UESXELNYBIOROE-QHCPKHFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
989	PDBBind:  1NL9	Ki: 1100 (nM) from 1 assay(s)
	BindingDB:  1NL9	Ki: min: 631, max: 1100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.192 
• R-Value Observed: 0.208 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.73	α = 90
b = 88.73	β = 90
c = 105.91	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: 2003-04-08 
Deposition Author(s): Szczepankiewicz, B.G., Liu, G., Hajduk, P.J., Abad-Zapatero, C., Pei, Z., Xin, Z., Lubben, T., Trevillyan, J.M., Stashko, M.A., Ballaron, S.J., Liang, H., Huang, F., Hutchins, C.W., Fesik, S.W., Jirousek, M.R.

Revision History  

• Version 1.0: 2003-04-08
  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