6WU8

Structure of human SHP2 in complex with inhibitor IACS-13909


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Allosteric SHP2 Inhibitor, IACS-13909, Overcomes EGFR-Dependent and EGFR-Independent Resistance Mechanisms toward Osimertinib.

Sun, Y.Meyers, B.A.Czako, B.Leonard, P.Mseeh, F.Harris, A.L.Wu, Q.Johnson, S.Parker, C.A.Cross, J.B.Di Francesco, M.E.Bivona, B.J.Bristow, C.A.Burke, J.P.Carrillo, C.C.Carroll, C.L.Chang, Q.Feng, N.Gao, G.Gera, S.Giuliani, V.Huang, J.K.Jiang, Y.Kang, Z.Kovacs, J.J.Liu, C.Y.Lopez, A.M.Ma, X.Mandal, P.K.McAfoos, T.Miller, M.A.Mullinax, R.A.Peoples, M.Ramamoorthy, V.Seth, S.Spencer, N.D.Suzuki, E.Williams, C.C.Yu, S.S.Zuniga, A.M.Draetta, G.F.Marszalek, J.R.Heffernan, T.P.Kohl, N.E.Jones, P.

(2020) Cancer Res 80: 4840-4853

  • DOI: https://doi.org/10.1158/0008-5472.CAN-20-1634
  • Primary Citation of Related Structures:  
    6WU8

  • PubMed Abstract: 

    Src homology 2 domain-containing phosphatase (SHP2) is a phosphatase that mediates signaling downstream of multiple receptor tyrosine kinases (RTK) and is required for full activation of the MAPK pathway. SHP2 inhibition has demonstrated tumor growth inhibition in RTK-activated cancers in preclinical studies. The long-term effectiveness of tyrosine kinase inhibitors such as the EGFR inhibitor (EGFRi), osimertinib, in non-small cell lung cancer (NSCLC) is limited by acquired resistance. Multiple clinically identified mechanisms underlie resistance to osimertinib, including mutations in EGFR that preclude drug binding as well as EGFR-independent activation of the MAPK pathway through alternate RTK (RTK-bypass). It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between multiple resistance mechanisms could restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. Here, we report the discovery of IACS-13909, a specific and potent allosteric inhibitor of SHP2, that suppresses signaling through the MAPK pathway. IACS-13909 potently impeded proliferation of tumors harboring a broad spectrum of activated RTKs as the oncogenic driver. In EGFR-mutant osimertinib-resistant NSCLC models with EGFR-dependent and EGFR-independent resistance mechanisms, IACS-13909, administered as a single agent or in combination with osimertinib, potently suppressed tumor cell proliferation in vitro and caused tumor regression in vivo . Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFRi-resistant NSCLC. SIGNIFICANCE: These findings highlight the discovery of IACS-13909 as a potent, selective inhibitor of SHP2 with drug-like properties, and targeting SHP2 may serve as a therapeutic strategy to overcome tumor resistance to osimertinib.


  • Organizational Affiliation

    TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas. ysun8@mdanderson.org.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
536Homo sapiensMutation(s): 0 
Gene Names: PTPN11PTP2CSHPTP2
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens)
Explore Q06124 
Go to UniProtKB:  Q06124
PHAROS:  Q06124
GTEx:  ENSG00000179295 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U9Y (Subject of Investigation/LOI)
Query on U9Y

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1-[3-(2,3-dichlorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine
C17 H18 Cl2 N6
AMADCPJVPLUGQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.671α = 90
b = 83.203β = 90
c = 217.701γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description