9VRR | pdb_00009vrr

Crystal structure of human PTPN2 with inhibitor WS3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.222 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.192 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9VRR

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 70.72 kDa 
  • Atom Count: 4,950 
  • Modeled Residue Count: 578 
  • Deposited Residue Count: 602 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ETL
(Subject of Investigation/LOI)

Query on A1ETL



Download:Ideal Coordinates CCD File
C [auth B],
D [auth A]
5-[2-fluoranyl-4-[1-(3-methylbutyl)azetidin-3-yl]-6-oxidanyl-phenyl]-1,1-bis(oxidanylidene)-1,2,5-thiadiazolidin-3-one
C16 H22 F N3 O4 S
DCGHMVNIHXCUSH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.222 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.192 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.8α = 90
b = 79.19β = 111.4
c = 81.131γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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