Structural basis for an allosteric Eya2 phosphatase inhibitor

Experimental Data Snapshot

  • Resolution: 3.17 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Structural and Functional Analyses of an Allosteric EYA2 Phosphatase Inhibitor That Has On-Target Effects in Human Lung Cancer Cells.

Anantharajan, J.Zhou, H.Zhang, L.Hotz, T.Vincent, M.Y.Blevins, M.A.Jansson, A.E.Kuan, J.W.L.Ng, E.Y.Yeo, Y.K.Baburajendran, N.Lin, G.Hung, A.W.Joy, J.Patnaik, S.Marugan, J.Rudra, P.Ghosh, D.Hill, J.Keller, T.H.Zhao, R.Ford, H.L.Kang, C.

(2019) Mol Cancer Ther 18: 1484-1496

  • DOI: https://doi.org/10.1158/1535-7163.MCT-18-1239
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    EYA proteins (EYA1-4) are critical developmental transcriptional cofactors that contain an EYA domain (ED) harboring Tyr phosphatase activity. EYA proteins are largely downregulated after embryogenesis but are reexpressed in cancers, and their Tyr phosphatase activity plays an important role in the DNA damage response and tumor progression. We previously identified a class of small-molecule allosteric inhibitors that specifically inhibit the Tyr phosphatase activity of EYA2. Herein, we determined the crystal structure of the EYA2 ED in complex with NCGC00249987 (a representative compound in this class), revealing that it binds to an induced pocket distant from the active site. NCGC00249987 binding leads to a conformational change of the active site that is unfavorable for Mg 2+ binding, thereby inhibiting EYA2's Tyr phosphatase activity. We demonstrate, using genetic mutations, that migration, invadopodia formation, and invasion of lung adenocarcinoma cells are dependent on EYA2 Tyr phosphatase activity, whereas growth and survival are not. Further, we demonstrate that NCGC00249987 specifically targets migration, invadopodia formation, and invasion of lung cancer cells, but that it does not inhibit cell growth or survival. The compound has no effect on lung cancer cells carrying an EYA2 F290Y mutant that abolishes compound binding, indicating that NCGC00249987 is on target in lung cancer cells. These data suggest that the NCGC00249987 allosteric inhibitor can be used as a chemical probe to study the function of the EYA2 Tyr phosphatase activity in cells and may have the potential to be developed into an antimetastatic agent for cancers reliant on EYA2's Tyr phosphatase activity.

  • Organizational Affiliation

    Experimental Drug Discovery Centre, A*STAR, Singapore, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eyes absent homolog 2A [auth B],
B [auth A],
294Homo sapiensMutation(s): 0 
Gene Names: EYA2EAB1
UniProt & NIH Common Fund Data Resources
Find proteins for O00167 (Homo sapiens)
Explore O00167 
Go to UniProtKB:  O00167
PHAROS:  O00167
GTEx:  ENSG00000064655 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00167
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9FX

Download Ideal Coordinates CCD File 
D [auth B],
E [auth A],
F [auth C]
C16 H11 F N4 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.17 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.985α = 90
b = 49.497β = 101.21
c = 144.957γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description