9YG3 | pdb_00009yg3

Targeting PTPN22 at non-orthosteric binding sites - a fragment approach

• PDB DOI: https://doi.org/10.2210/pdb9YG3/pdb

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


• Deposited: 2025-09-27 Released: 2026-01-28 
• Deposition Author(s): Di Lello, P., Wells, M.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Targeting PTPN22 at Nonorthosteric Binding Sites - A Fragment Approach

Di Lello, P., Wells, M.M., Davis, B., Daniels, Z., Garner, T.P., Gazzard, L., Harris, R., Hubbard, R.E., Landry, M.L., Martin, B., Morgan, J.L.W., Patapoff, A., Simmonite, H., Skelton, N., Ultsch, M., Walters, B.T., Wu, P., Dimitrova, Y.N., Huard, K.

(2026) ACS Omega 11: 3465-3480

• DOI: https://doi.org/10.1021/acsomega.5c11028

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.2 kDa 
• Atom Count: 5,257 
• Modeled Residue Count: 597 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 22	A, B	309	Homo sapiens	Mutation(s): 0  Gene Names: PTPN22, PTPN8 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R2 (Homo sapiens) Explore Q9Y2R2  Go to UniProtKB:  Q9Y2R2
PHAROS:  Q9Y2R2 GTEx:  ENSG00000134242

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	C [auth A], E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.56	α = 90
b = 46.42	β = 101.6
c = 122.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Di Lello, P., Wells, M.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release