9P6A | pdb_00009p6a

The catalytic domain of MEKK2 in complex with ponatinib

• PDB DOI: https://doi.org/10.2210/pdb9P6A/pdb

• 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

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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

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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.6 kDa 
• Atom Count: 4,108 
• Modeled Residue Count: 500 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 2	A, B	299	Homo sapiens	Mutation(s): 0  Gene Names: MAP3K2, MAPKKK2, MEKK2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LI (Subject of Investigation/LOI)	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) 

Diffraction Data: https://doi.org/10.15785/SBGRID/1187

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.3	α = 90
b = 91.3	β = 90
c = 145.23	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Vish, K.J., Boggon, T.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	F31HL165968
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS134606
American Heart Association	United States	961309

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release