Limits...
Crystal structures of the S6K1 kinase domain in complexes with inhibitors.

Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S - J. Struct. Funct. Genomics (2014)

Bottom Line: Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123.Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein.The structural features required for the specific binding of inhibitors are discussed.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.

ABSTRACT
Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. The crystal structures of the five inhibitors in complexes with the S6K1 kinase domain were determined at resolutions between 1.85 and 2.10 Å. All of the inhibitors bound to the ATP binding site, lying along the P-loop, while the activation loop stayed in the inactive form. Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123. Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed.

Show MeSH

Related in: MedlinePlus

Structure of S6K1KD·F176. a The protein is shown as a ribbon model in cyan, with the P-loop and the strands β1 and β2 in green, helix αC in pale blue, the hinge region in orange, and the activation loop in pink. The phosphorylated Thr252 is depicted by red sticks, and the zinc ion is a red sphere. The bound inhibitor (F176) is shown in magenta. b Superimposition of the Cα traces of the six protein structures. The structures are colored as follows: cyan, S6K1KD·PF-4708671; green, S6K1KD·F108; blue, S6K1KD·F109; magenta, S6K1KD·F179; yellow, S6K1KD·F176; pink, S6K1KD·F177. c X-ray fluorescence measurement from an S6K1KD·F179 crystal
© Copyright Policy - OpenAccess
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4125821&req=5

Fig2: Structure of S6K1KD·F176. a The protein is shown as a ribbon model in cyan, with the P-loop and the strands β1 and β2 in green, helix αC in pale blue, the hinge region in orange, and the activation loop in pink. The phosphorylated Thr252 is depicted by red sticks, and the zinc ion is a red sphere. The bound inhibitor (F176) is shown in magenta. b Superimposition of the Cα traces of the six protein structures. The structures are colored as follows: cyan, S6K1KD·PF-4708671; green, S6K1KD·F108; blue, S6K1KD·F109; magenta, S6K1KD·F179; yellow, S6K1KD·F176; pink, S6K1KD·F177. c X-ray fluorescence measurement from an S6K1KD·F179 crystal

Mentions: The crystal structures of S6K1KD with the inhibitors exhibited the typical bilobal structures of protein kinases, and the inhibitors occupied the ATP-binding pocket between the small N-terminal lobe and the large C-terminal lobe (e.g. F176 in Fig. 2a). Although the F176 and F177 complexes were crystallized in a different packing mode from that of the others, they shared similar overall conformations (Fig. 2b). The F179 complex has a different αC conformation as compared with the others, as described below in detail. Correspondingly, the Cα root mean square deviation (rmsd) values of the structures of the F108, F109, F176, F177, and F179 complexes with that of the PF-4708671 complex are 0.43, 0.41, 0.69, 0.70, and 1.05 Å, respectively, indicating a slightly larger difference for the F179 complex structure. The F108 and F109 complex structures were almost identical to each other (Cα rmsd value, 0.27 Å), and so were the F176 and F177 complex structures (Cα rmsd value, 0.17 Å).Fig. 2


Crystal structures of the S6K1 kinase domain in complexes with inhibitors.

Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S - J. Struct. Funct. Genomics (2014)

Structure of S6K1KD·F176. a The protein is shown as a ribbon model in cyan, with the P-loop and the strands β1 and β2 in green, helix αC in pale blue, the hinge region in orange, and the activation loop in pink. The phosphorylated Thr252 is depicted by red sticks, and the zinc ion is a red sphere. The bound inhibitor (F176) is shown in magenta. b Superimposition of the Cα traces of the six protein structures. The structures are colored as follows: cyan, S6K1KD·PF-4708671; green, S6K1KD·F108; blue, S6K1KD·F109; magenta, S6K1KD·F179; yellow, S6K1KD·F176; pink, S6K1KD·F177. c X-ray fluorescence measurement from an S6K1KD·F179 crystal
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4125821&req=5

Fig2: Structure of S6K1KD·F176. a The protein is shown as a ribbon model in cyan, with the P-loop and the strands β1 and β2 in green, helix αC in pale blue, the hinge region in orange, and the activation loop in pink. The phosphorylated Thr252 is depicted by red sticks, and the zinc ion is a red sphere. The bound inhibitor (F176) is shown in magenta. b Superimposition of the Cα traces of the six protein structures. The structures are colored as follows: cyan, S6K1KD·PF-4708671; green, S6K1KD·F108; blue, S6K1KD·F109; magenta, S6K1KD·F179; yellow, S6K1KD·F176; pink, S6K1KD·F177. c X-ray fluorescence measurement from an S6K1KD·F179 crystal
Mentions: The crystal structures of S6K1KD with the inhibitors exhibited the typical bilobal structures of protein kinases, and the inhibitors occupied the ATP-binding pocket between the small N-terminal lobe and the large C-terminal lobe (e.g. F176 in Fig. 2a). Although the F176 and F177 complexes were crystallized in a different packing mode from that of the others, they shared similar overall conformations (Fig. 2b). The F179 complex has a different αC conformation as compared with the others, as described below in detail. Correspondingly, the Cα root mean square deviation (rmsd) values of the structures of the F108, F109, F176, F177, and F179 complexes with that of the PF-4708671 complex are 0.43, 0.41, 0.69, 0.70, and 1.05 Å, respectively, indicating a slightly larger difference for the F179 complex structure. The F108 and F109 complex structures were almost identical to each other (Cα rmsd value, 0.27 Å), and so were the F176 and F177 complex structures (Cα rmsd value, 0.17 Å).Fig. 2

Bottom Line: Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123.Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein.The structural features required for the specific binding of inhibitors are discussed.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.

ABSTRACT
Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. The crystal structures of the five inhibitors in complexes with the S6K1 kinase domain were determined at resolutions between 1.85 and 2.10 Å. All of the inhibitors bound to the ATP binding site, lying along the P-loop, while the activation loop stayed in the inactive form. Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123. Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed.

Show MeSH
Related in: MedlinePlus