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 8SKL | pdb_00008skl

PTP1B in complex with 182


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.194 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8SKL

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

A small molecule inhibitor of PTP1B and PTPN2 enhances T cell anti-tumor immunity.

Liang, S., Tran, E., Du, X., Dong, J., Sudholz, H., Chen, H., Qu, Z., Huntington, N.D., Babon, J.J., Kershaw, N.J., Zhang, Z.Y., Baell, J.B., Wiede, F., Tiganis, T.

(2023) Nat Commun 14: 4524-4524

  • DOI: https://doi.org/10.1038/s41467-023-40170-8
  • Primary Citation Related Structures: 
    8SKL

  • PubMed Abstract: 

    The inhibition of protein tyrosine phosphatases 1B (PTP1B) and N2 (PTPN2) has emerged as an exciting approach for bolstering T cell anti-tumor immunity. ABBV-CLS-484 is a PTP1B/PTPN2 inhibitor in clinical trials for solid tumors. Here we have explored the therapeutic potential of a related small-molecule-inhibitor, Compound-182. We demonstrate that Compound-182 is a highly potent and selective active site competitive inhibitor of PTP1B and PTPN2 that enhances T cell recruitment and activation and represses the growth of tumors in mice, without promoting overt immune-related toxicities. The enhanced anti-tumor immunity in immunogenic tumors can be ascribed to the inhibition of PTP1B/PTPN2 in T cells, whereas in cold tumors, Compound-182 elicited direct effects on both tumor cells and T cells. Importantly, treatment with Compound-182 rendered otherwise resistant tumors sensitive to α-PD-1 therapy. Our findings establish the potential for small molecule inhibitors of PTP1B and PTPN2 to enhance anti-tumor immunity and combat cancer.


  • Organizational Affiliation: 
    • Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 38.19 kDa 
  • Atom Count: 2,716 
  • Modeled Residue Count: 299 
  • Deposited Residue Count: 322 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1322Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V2O
(Subject of Investigation/LOI)

Query on V2O



Download:Ideal Coordinates CCD File
E [auth A]5-[1-fluoro-3-hydroxy-7-(3-hydroxy-3-methylbutoxy)naphthalen-2-yl]-1lambda~6~,2,5-thiadiazolidine-1,1,3-trione
C17 H19 F N2 O6 S
KJYRSQLWJMEJNM-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
V2O BindingDB:  8SKL IC50: 0.63 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.194 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.961α = 90
b = 87.961β = 90
c = 104.345γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedAustralia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-12-04
    Changes: Structure summary