7UAD

Crystal structure of human PTPN2 with inhibitor ABBV-CLS-484


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity.

Baumgartner, C.K.Ebrahimi-Nik, H.Iracheta-Vellve, A.Hamel, K.M.Olander, K.E.Davis, T.G.R.McGuire, K.A.Halvorsen, G.T.Avila, O.I.Patel, C.H.Kim, S.Y.Kammula, A.V.Muscato, A.J.Halliwill, K.Geda, P.Klinge, K.L.Xiong, Z.Duggan, R.Mu, L.Yeary, M.D.Patti, J.C.Balon, T.M.Mathew, R.Backus, C.Kennedy, D.E.Chen, A.Longenecker, K.Klahn, J.T.Hrusch, C.L.Krishnan, N.Hutchins, C.W.Dunning, J.P.Bulic, M.Tiwari, P.Colvin, K.J.Chuong, C.L.Kohnle, I.C.Rees, M.G.Boghossian, A.Ronan, M.Roth, J.A.Wu, M.J.Suermondt, J.S.M.T.Knudsen, N.H.Cheruiyot, C.K.Sen, D.R.Griffin, G.K.Golub, T.R.El-Bardeesy, N.Decker, J.H.Yang, Y.Guffroy, M.Fossey, S.Trusk, P.Sun, I.M.Liu, Y.Qiu, W.Sun, Q.Paddock, M.N.Farney, E.P.Matulenko, M.A.Beauregard, C.Frost, J.M.Yates, K.B.Kym, P.R.Manguso, R.T.

(2023) Nature 622: 850-862

  • DOI: https://doi.org/10.1038/s41586-023-06575-7
  • Primary Citation of Related Structures:  
    7UAD

  • PubMed Abstract: 

    Immune checkpoint blockade is effective for some patients with cancer, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance 1,2 . The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour cells or immune cells promotes anti-tumour immunity 3-6 . However, phosphatases are challenging drug targets; in particular, the active site has been considered undruggable. Here we present the discovery and characterization of ABBV-CLS-484 (AC484), a first-in-class, orally bioavailable, potent PTPN2 and PTPN1 active-site inhibitor. AC484 treatment in vitro amplifies the response to interferon and promotes the activation and function of several immune cell subsets. In mouse models of cancer resistant to PD-1 blockade, AC484 monotherapy generates potent anti-tumour immunity. We show that AC484 inflames the tumour microenvironment and promotes natural killer cell and CD8 + T cell function by enhancing JAK-STAT signalling and reducing T cell dysfunction. Inhibitors of PTPN2 and PTPN1 offer a promising new strategy for cancer immunotherapy and are currently being evaluated in patients with advanced solid tumours (ClinicalTrials.gov identifier NCT04777994 ). More broadly, our study shows that small-molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to or exceeding that of antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge, AC484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics that target this important class of enzymes.


  • Organizational Affiliation

    AbbVie, North Chicago, IL, USA. christina.baumgartner@abbvie.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 2324Homo 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
M5R (Subject of Investigation/LOI)
Query on M5R

Download Ideal Coordinates CCD File 
B [auth A]5-{(7R)-1-fluoro-3-hydroxy-7-[(3-methylbutyl)amino]-5,6,7,8-tetrahydronaphthalen-2-yl}-1lambda~6~,2,5-thiadiazolidine-1,1,3-trione
C17 H24 F N3 O4 S
DVFCRTGTEXUFIN-GFCCVEGCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.65α = 90
b = 142.78β = 90
c = 77.95γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-18
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Database references