9VRS | pdb_00009vrs

Crystal structure of human PTPN2 with inhibitor WS19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Development of Novel PTPN2/1 Inhibitors for the Treatment of Melanoma.

Wang, D.Song, M.Tong, C.Wang, W.Li, Q.Liu, J.Chen, A.Chen, Y.Wang, L.Hao, H.Wang, X.Han, K.Xiao, Y.Kuang, W.Yang, P.

(2025) J Med Chem 68: 21917-21938

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02300
  • Primary Citation of Related Structures:  
    9VRR, 9VRS

  • PubMed Abstract: 

    The global incidence of melanoma has risen substantially over the past two decades, driving an urgent need for novel therapeutic strategies. The nonreceptor protein tyrosine phosphatases PTPN2/PTPN1 have emerged as promising therapeutic targets, yet developing effective inhibitors faces significant drug-like property challenges. Through rational drug design, we discovered WS35 ─a potent dual PTPN2/1 inhibitor exhibiting exceptional enzymatic activity (PTPN2 IC 50 = 5.8 nM, PTPN1 IC 50 = 12.8 nM), favorable safety profiles, and enhanced oral bioavailability (F = 7.1%). Mechanistic studies demonstrate that WS35 modulates the IFNγ-JAK-STAT signaling axis, significantly augmenting CD8 + T-cell tumor infiltration. In B16-OVA syngeneic models, WS35 monotherapy and its combination with an anti-PD-1 antibody achieved robust tumor growth suppression, outperforming AC484, with no observable systemic toxicity. Collectively, WS35 represents a preclinical candidate with validated efficacy and safety for developing novel antimelanoma therapeutics.


  • Organizational Affiliation
    • State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 2A [auth B],
B [auth A]
301Homo sapiensMutation(s): 0 
Gene Names: PTPN2PTPT
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P17706 (Homo sapiens)
Explore P17706 
Go to UniProtKB:  P17706
PHAROS:  P17706
GTEx:  ENSG00000175354 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17706
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ETK (Subject of Investigation/LOI)
Query on A1ETK

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
5-[2-fluoranyl-6-oxidanyl-4-(4,5,6,7-tetrahydropyrazolo[1,5-a]pyridin-3-yl)phenyl]-1,1-bis(oxidanylidene)-1,2,5-thiadiazolidin-3-one
C15 H15 F N4 O4 S
SQZMXWLMZXXUEK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60α = 90
b = 78.81β = 111.73
c = 80.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-12-17 
  • Deposition Author(s): Tong, C.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82304296

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release