9P6A | pdb_00009p6a

The catalytic domain of MEKK2 in complex with ponatinib

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2025-06-18 Released: 2025-11-26 
  • Deposition Author(s): Vish, K.J., Boggon, T.J.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), American Heart Association

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for MEKK2 dimerization and substrate recognition.

Vish, K.J.Huet-Calderwood, C.Ha, B.H.Calderwood, D.A.Boggon, T.J.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-66884-5
  • Primary Citation of Related Structures:  
    9P6A

  • PubMed Abstract: 

    Signaling downstream of Mitogen-Activated Protein Kinase Kinase Kinases (MAP3K) is promiscuous. In the vascular and immune systems the MAP3K, MEKK2, activates different substrates, but the mechanisms of substrate targeting have not been delineated. Here, we determine the 2.4 Å crystal structure of the MEKK2 kinase domain in complex with the small molecule inhibitor, ponatinib. We find that MEKK2 dimerizes by a surface centered on the αG helix and the C-terminal region of the activation segment, that this surface is important for MEKK2 autophosphorylation and dimerization, and that this surface is conserved with MEKK3. We then assess the importance of the surface for phosphorylation and recruitment of two MAP2K substrates, MEK5 and MKK6. We find that both MEK5 and MKK6 require the αG helix-mediated interaction for phosphorylation. In contrast, MEKK2 recruitment of MEK5 is dependent on PB1 domain interactions but MKK6 recruitment is associated with the αG helix-mediated interaction. Our study therefore provides a framework to understand diverse substrate targeting by the MAP3Ks, MEKK2 and MEKK3.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 2
A, B
299Homo sapiensMutation(s): 0 
Gene Names: MAP3K2MAPKKK2MEKK2
EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U5 (Homo sapiens)
Explore Q9Y2U5 
Go to UniProtKB:  Q9Y2U5
PHAROS:  Q9Y2U5
GTEx:  ENSG00000169967 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2U5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0LI (Subject of Investigation/LOI)
Query on 0LI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide
C29 H27 F3 N6 O
PHXJVRSECIGDHY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.3α = 90
b = 91.3β = 90
c = 145.23γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF31HL165968
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS134606
American Heart AssociationUnited States961309

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references