Crystal structure of human calcium/calmodulin-dependent protein kinase kinase 2, beta, CaMKK2 kinase domain in complex with STO-609

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 

Starting Model: experimental
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Crystal structure of the Ca2+/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609

Kukimoto-Niino, M.Yoshikawa, S.Takagi, T.Ohsawa, N.Tomabechi, Y.Terada, T.Shirouzu, M.Suzuki, A.Lee, S.Yamauchi, T.Okada-Iwabu, M.Iwabu, M.Kadowaki, T.Minokoshi, Y.Yokoyama, S.

(2011) J Biol Chem 286: 22570-22579

  • DOI: https://doi.org/10.1074/jbc.M111.251710
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ca(2+)/calmodulin (CaM)-dependent protein kinase (CaMK) kinase (CaMKK) is a member of the CaMK cascade that mediates the response to intracellular Ca(2+) elevation. CaMKK phosphorylates and activates CaMKI and CaMKIV, which directly activate transcription factors. In this study, we determined the 2.4 Å crystal structure of the catalytic kinase domain of the human CaMKKβ isoform complexed with its selective inhibitor, STO-609. The structure revealed that CaMKKβ lacks the αD helix and that the equivalent region displays a hydrophobic molecular surface, which may reflect its unique substrate recognition and autoinhibition. Although CaMKKβ lacks the activation loop phosphorylation site, the activation loop is folded in an active-state conformation, which is stabilized by a number of interactions between amino acid residues conserved among the CaMKK isoforms. An in vitro analysis of the kinase activity confirmed the intrinsic activity of the CaMKKβ kinase domain. Structure and sequence analyses of the STO-609-binding site revealed amino acid replacements that may affect the inhibitor binding. Indeed, mutagenesis demonstrated that the CaMKKβ residue Pro(274), which replaces the conserved acidic residue of other protein kinases, is an important determinant for the selective inhibition by STO-609. Therefore, the present structure provides a molecular basis for clarifying the known biochemical properties of CaMKKβ and for designing novel inhibitors targeting CaMKKβ and the related protein kinases.

  • Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase kinase 2298Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RR4 (Homo sapiens)
Explore Q96RR4 
Go to UniProtKB:  Q96RR4
GTEx:  ENSG00000110931 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RR4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 609

Download Ideal Coordinates CCD File 
B [auth A]7-oxo-7H-benzimidazo[2,1-a]benz[de]isoquinoline-3-carboxylic acid
C19 H10 N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
609 PDBBind:  2ZV2 IC50: 500 (nM) from 1 assay(s)
BindingDB:  2ZV2 IC50: min: 10, max: 2.42e+4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.368α = 90
b = 77.153β = 90
c = 84.332γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description