Primary Citation PubMed: 16794575
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Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites.
(2008) EMBO J 27
PubMed: 18239682 | PubMedCentral: PMC2239268 | DOI: 10.1038/emboj.2008.8
( B ) Comparison of the activation segments of SLK (green), LOK (orange), DAPK3A (cyan) and CHK2 (magenta; PDB: 2CN5) after superimposition.
Table 2 Dimer interfaces SLK SLK-diP LOK a DAPK3 a CHK2 PDB code 2J51 2JFL 2J7T 2J90 2CN5 Dimer type (N/C) b C C C N C Interface-accessible surface area per monomer (ASA; Å 2 ) c 1735 2032 1730 1940 1335 % ASA c 11.5 13 11.5 12.9 8.5 Interface residues (atoms) c 48 (181) 55 (212) 46 (176) 56 (210) 39 (139) % Polar atoms in interface d 32 34 28 32 30 % Nonpolar atoms in interface d 68 66 72 68 70 Length/breadth of interface (Å) d 61/32 61/28 47/22 52/33 52/23 Salt bridges c 2 2 4 3 2 Direct hydrogen bonds c 18 29 23 21 14 a LOK and DAPK3 (molA) have incomplete activation loop regions due to disorder and the extent of the dimer interface is therefore likely to be under-represented by the values shown.
Publication Year: 2008
Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays.
(2011) PLoS One 6
PubMed: 21390216 | PubMedCentral: PMC3044726 | DOI: 10.1371/journal.pone.0016903
The two kinases that fulfilled these criteria and were thus chosen as templates belong to the CAMK kinase family  , have a 32% sequence identity with the kinase domain of h... KK-2, have a 50% identity with the residues of the ATP-binding site of hIKK-2 (where these residues correspond to those in the G-loop, hinge region, HRD motif and catalytic loop); they are the serine/threonine-protein kinase CHK2 (PDB code 2CN5  ) and the death-associated protein kinase 3 or ZIP kinase (PDB code 2J90  ).
The superposition of both template structures revealed some differences in their loop structures: (a) the G-loop is more open in 2J90 than in 2CN5 and (b) the A-loop coordinates were not present for 2J90.
Because we were interested in finding new ATP-competitive inhibitors for hIKK-2, we selected two kinase structures as templates (2CN5  and 2J90  ), each cocrystallized with a different ATP-competitive inhibitor (ADP and pyridone 6, respectively), both sharing a 32% sequence identity with the kinase domain of hIKK-2 and a 50% identity with the residues of the ATP-binding site of hIKK-2 (where these residues correspond to those in the G-loop, hinge region, HRD motif and catalytic loop).
Publication Year: 2011
Benzimidazole inhibitors of the protein kinase CHK2: clarification of the binding mode by flexible side chain docking and protein-ligand crystallography.
(2012) Bioorg Med Chem 20
PubMed: 23058106 | PubMedCentral: PMC3778940 | DOI: 10.1016/j.bmc.2012.09.024
49 4.3 Protein crystal structure preparation CHK2 crystal structures (PDB ID: 2CN5 and 2W0J) representing different ligand binding modes were obtained from the Protein databank.
Figure 2 Binding of (A) ADP to CHK2 (PDB ID: 2CN5 ) 42 and (B) NSC109555 to CHK2 (PDB ID: 2W0J ).
15–17 We chose the structures of CHK2 bound to ADP (PDB ID: 2CN5 ) and to NSC1095555 (PDB ID: 2W0J ) as representative high resolution parent structures for docking [2.25 and 2.05 Å, respectively].
Figure 3 Number of polar interactions formed by: (A) Ligands which docked via the hinge to the apo-structure derived from the ADP-bound structure (PDB ID: 2CN5 ) (B).
In the structure representing the ADP-bound CHK2 conformation (PDB ID: 2CN5 ), hydrogen bond interactions with both Glu302 and Met304 were observed for the lowest energy poses of 14 active compounds (compounds: 1, 13 , 15 , 16 , 18 , 19 , 20 , 22 , 30 , 33 , 38 , 39 , 47 and 59 ); the other 36 compounds did not make these interactions.
In summary, an unconstrained rigid docking protocol yielded a higher hit rate when applied to the NSC109555-derived protein structure 2W0J versus the ADP-derived protein structure 2CN5; however, neither protein structure provides binding mode solutions consistent with the importance of interactions from all 4 polar atoms of the benzimidazole–carboxamide scaffold, as demonstrated by the experimental SAR ( vide supra and Table 1 ).
In brief, we first applied a distance cut-off, based upon our rigid docking results for protein structures 2CN5 and 2W0J, to include all protein residues of the respective ligand-binding site with the potential to be treated as flexible.
Application of these criteria reduced the number of selected residues to 16 and 27 in the 2CN5 and 2W0J structures, respectively ( Table S2, Supplementary data ).
The search space was defined by locating the centre of the ligand present in each crystal structure (ADP for structure 2CN5 and NSC109555 for structure 2W0J) and using a radius of 16 Å from the centroid to define the volume of the binding pocket searched during docking.
2.3 Flexible docking of benzimidazole inhibitors We hypothesised that rigid docking may preclude the optimal orientation of protein side chains in the ATP binding site and applied a docking protocol incorporating side chain flexibility to both binding modes of CHK2 exemplified by protein structures 2W0J and 2CN5.
Publication Year: 2012
Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2.
(2014) Elife 3
PubMed: 24867643 | PubMedCentral: PMC4032492 | DOI: null
Shown are SLK phosphorylated or non-phosphorylated (PDB IDs 2JFL and 2J51, respectively, both bound to triazole inhibitor DKI), Chk2 (PDB ID 2CN5 bound to ADP), LOK (PDB ID 2 J7T bound to SU11274), DA... K3 (PDB ID 2J90 bound to pyridone 6), p70S6K1 (PDB ID 3A60 bound to staurosporine), and OSR1 (PDB ID 3DAK bound to AMPPNP).
Oliver AW , Paul A , Boxall KJ , Barrie SE , Aherne GW , Garrett MD , Mittnacht S , Pearl LH , 2006 , Crystal structure of human Ck2 in complex with ADP , http://www.pdb.org/pdb/explore/explore.do?structureId=2cn5 , Publicly available at RCSB Protein Data Bank.
Publication Year: 2014
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