9ZME | pdb_00009zme

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 2

• PDB DOI: https://doi.org/10.2210/pdb9ZME/pdb

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


• Deposited: 2025-12-10 Released: 2026-05-27 
• Deposition Author(s): Palte, R.L., Schneider, S.E., Candito, D.A., Zheng, X.M., Huang, H., Stinn, A., Lindner, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.203 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Discovery of Potent and Selective Benzothiophene Difluoromethyl Phosphonate (DFMP) PTPN2/N1-Dual Inhibitors.

Zheng, X.M., Candito, D.A., Jewell, J., Childers, M., Kawamura, S., Logan, K.M., Otte, R.D., Yeung, C.S., Xiao, D., Liu, P., DeMong, D.E., Huang, C., Sanyal, S., McGowan, M., Levi, S.M., Schneider, S.E., Fradera, X., Palte, R.L., Lyons, T.W., Poremba, K.E., Miller, J.R., Chai, X., Xu, Z., Musisi, I., Mansueto, M.S., Venkataraman, S., Moy, L.Y., Zhang, M., Yang, Y., Cheng, M., McLeod, R., Laskey, J., Angagaw, M., Smith, D.M., Varkhede, N., Muise, E.S., Bass, A., Walraven, J., Doty, A., Yu, H., Rath, B., Engstrom, L., Wang, H., Follmer, N.E., Slavonic, M., Ehrenberger, T., Nicholson, B., Haining, W.N., Bennett, D.J., DiMauro, E.F., Machacek, M.R., Shumway, S.

(2026) J Med Chem 69: 10515-10530

• PubMed: 42054654 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c03738
• Primary Citation Related Structures: 
  9ZME, 9ZMF, 9ZMG, 9ZMH


• PubMed Abstract: 
  

  PTPN1 and PTPN2 are interesting targets for immuno-oncology due to their ability to modulate IFNγ signaling and T-cell activity. We report the discovery of benzothiophene difluoromethyl phosphonate (DFMP) inhibitors with potent dual PTPN1/PTPN2 activity. Structure-based design and a late-stage Ir-catalyzed C-H borylation enabled C5/C7-disubstituted designs that produced a marked inflection in potency. Systematic vector optimization improved potency, selectivity, and pharmacokinetic properties. Mechanistic studies identified SLC19A1 as a key transporter mediating cellular uptake. Lead compound 25 exhibited good potency, high selectivity, favorable PK, and dose-dependent pSTAT1 induction in a MC38 mouse model. These results establish compound 25 as promising structurally differentiated tool to study PTPN1/N2 inhibition and underscore the importance of SLC19A1 in the transport of DFMPs.

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Organizational Affiliation: 
• Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.32 kDa 
• Atom Count: 2,733 
• Modeled Residue Count: 301 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	333	Homo sapiens	Mutation(s): 0  Gene Names: 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 GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1C3A( Subject of Investigation/LOI)	B [auth A]	{[3-bromo-7-(3-hydroxy-3-methylbutoxy)naphthalen-2-yl]di(fluoro)methyl}phosphonic acid C16 H18 Br F2 O5 P NZJOUUYUQIOMFI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.203 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.254	α = 90
b = 88.254	β = 90
c = 103.843	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Palte, R.L., Schneider, S.E., Candito, D.A., Zheng, X.M., Huang, H., Stinn, A., Lindner, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release