9UZT | pdb_00009uzt

Crystal structure of human PTPN2 with inhibitor K-38


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Literature

Targeting Protein Tyrosine Phosphatase Nonreceptor Type 2 with a Novel Inhibitor for the Treatment of Melanoma.

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

(2025) J Med Chem 68: 24649-24671

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02622
  • Primary Citation of Related Structures:  
    9UZT

  • PubMed Abstract: 

    Melanoma is a highly aggressive skin cancer with strong metastatic potential, posing significant clinical challenges. Currently, melanoma treatment commonly includes chemotherapy and immunotherapy; nevertheless, the treatment modalities have specific limitations. PTPN2 (protein tyrosine phosphatase nonreceptor type 2) has emerged as a promising therapeutic target. Through rational drug design, we identified compound K-38 , a potent PTPN2 inhibitor (IC 50 = 7.05 nM) with high safety (hERG IC 50 > 40 μM) and excellent liver metabolic stability ( T 1/2 = 408 min). Compound K-38 also showed improved oral bioavailability ( F = 10.46%) over AC-484 ( F = 1.40%) (Zheng European Journal of Medicinal Chemistry 2024, 270, 116390, ). In vivo, compound K-38 significantly suppressed melanoma growth, especially when combined with anti-PD-1 therapy, outperforming AC-484 . It enhanced lymphocyte infiltration into tumors and modulated IFN-γ signaling pathways. These findings indicate that compound K-38 is a potent small molecule inhibitor of PTPN2, laying the groundwork for the future development of PTPN2-targeted 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]300Homo 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
A1EQR (Subject of Investigation/LOI)
Query on A1EQR

Download Ideal Coordinates CCD File 
B
~{N}-cycloheptyl-4-[3-fluoranyl-5-oxidanyl-4-[1,1,4-tris(oxidanylidene)-1,2,5-thiadiazolidin-2-yl]phenyl]-1~{H}-imidazole-2-carboxamide
C19 H22 F N5 O5 S
RYAIQNKSHNFQJM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.95α = 90
b = 94.95β = 90
c = 100.514γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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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)China--

Revision History  (Full details and data files)

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