6S75

Crystal structure of Nek7 bound to compound 51

Summary for 6S75

• Entry DOI: 10.2210/pdb6s75/pdb
• Related: 6S73 6S76
• Descriptor: Serine/threonine-protein kinase Nek7, 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide (2 entities in total)
• Functional Keywords: kinase, inhibitor, cell cycle
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 144143.31

Authors

Nasir, N.,Bayliss, R. (deposition date: 2019-07-04, release date: 2020-06-10, Last modification date: 2024-01-24)

Primary citation

Byrne, M.J.,Nasir, N.,Basmadjian, C.,Bhatia, C.,Cunnison, R.F.,Carr, K.H.,Mas-Droux, C.,Yeoh, S.,Cano, C.,Bayliss, R.
Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine.
Biochem.J., 477:1525-1539, 2020

PubMed Abstract: Nek7 is a serine/threonine-protein kinase required for proper spindle formation and cytokinesis. Elevated Nek7 levels have been observed in several cancers, and inhibition of Nek7 might provide a route to the development of cancer therapeutics. To date, no selective and potent Nek7 inhibitors have been identified. Nek7 crystal structures exhibit an improperly formed regulatory-spine (R-spine), characteristic of an inactive kinase. We reasoned that the preference of Nek7 to crystallise in this inactive conformation might hinder attempts to capture Nek7 in complex with Type I inhibitors. Here, we have introduced aromatic residues into the R-spine of Nek7 with the aim to stabilise the active conformation of the kinase through R-spine stacking. The strong R-spine mutant Nek7SRS retained catalytic activity and was crystallised in complex with compound 51, an ATP-competitive inhibitor of Nek2 and Nek7. Subsequently, we obtained the same crystal form for wild-type Nek7WT in apo form and bound to compound 51. The R-spines of the three well-ordered Nek7WT molecules exhibit variable conformations while the R-spines of the Nek7SRS molecules all have the same, partially stacked configuration. Compound 51 bound to Nek2 and Nek7 in similar modes, but differences in the precise orientation of a substituent highlights features that could be exploited in designing inhibitors that are selective for particular Nek family members. Although the SRS mutations are not required to obtain a Nek7-inhibitor structure, we conclude that it is a useful strategy for restraining the conformation of a kinase in order to promote crystallogenesis.

PubMed: 32242624
DOI: 10.1042/BCJ20200128

Experimental method

X-RAY DIFFRACTION (3.3 Å)