8S6I | pdb_00008s6i

Crystal structure of the human CDKL2 kinase domain with Compound 9

• PDB DOI: https://doi.org/10.2210/pdb8S6I/pdb

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


• Deposited: 2024-02-27 Released: 2025-02-26 
• Deposition Author(s): Chen, X., Ni, X., Brooke, L., Bullock, A.N.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.222 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2.

Bashore, F.M., Min, S.M., Chen, X., Howell, S., Rinderle, C.H., Morel, G., Silvaroli, J.A., Wells, C.I., Bunnell, B.A., Drewry, D.H., Pabla, N.S., Ultanir, S.K., Bullock, A.N., Axtman, A.D.

(2024) ACS Med Chem Lett 15: 1325-1333

• PubMed: 39140040 
• DOI: https://doi.org/10.1021/acsmedchemlett.4c00219
• Primary Citation Related Structures: 
  8S6I


• PubMed Abstract: 
  

  Acylaminoindazole-based inhibitors of CDKL2 were identified via analyses of cell-free binding and selectivity data. Compound 9 was selected as a CDKL2 chemical probe based on its potent inhibition of CDKL2 enzymatic activity, engagement of CDKL2 in cells, and excellent kinome-wide selectivity, especially when used in cells. Compound 16 was designed as a negative control to be used alongside compound 9 in experiments to interrogate CDKL2-mediated biology. A solved cocrystal structure of compound 9 bound to CDKL2 highlighted key interactions it makes within its ATP-binding site. Inhibition of downstream phosphorylation of EB2, a CDKL2 substrate, in rat primary neurons provided evidence that engagement of CDKL2 by compound 9 in cells resulted in inhibition of its activity. When used at relevant concentrations, compound 9 does not impact the viability of rat primary neurons or certain breast cancer cells nor elicit consistent changes in the expression of proteins involved in epithelial-mesenchymal transition.

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Organizational Affiliation: 
• Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.
Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States.
Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K.
Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States.
UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.04 kDa 
• Atom Count: 2,627 
• Modeled Residue Count: 302 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase-like 2	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CDKL2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q92772 (Homo sapiens) Explore Q92772  Go to UniProtKB:  Q92772
PHAROS:  Q92772 GTEx:  ENSG00000138769

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H5G (Subject of Investigation/LOI)	B [auth A]	~{N}-[6-[3-[(2-methylpropylsulfonylamino)methyl]phenyl]-1~{H}-indazol-3-yl]cyclopropanecarboxamide C22 H26 N4 O3 S IIKPYJZUOZRTIB-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.093	α = 90
b = 58.093	β = 90
c = 104.261	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2.multiplex	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Chen, X., Ni, X., Brooke, L., Bullock, A.N.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release