3WE4: S6K1 kinase domain

Crystal structure of S6K1 kinase domain in complex with a pyrimidine derivative PF-4708671 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole. Determined by X-ray diffraction at 2.0 Å resolution. Released 6 Aug 2014.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,498
Mol. weight: 37.63 kDa
Ligands: 5FI, ZN
Released: 6 Aug 2014

Explore 3WE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WE4 contains 18 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	88-90	3
β-strand	91-99	9	1
β-strand	103-110	8	1
β-strand	119-126	8	1
α-helix	127-131	5
α-helix	134-149	16
β-strand	155	1	2
α-helix	156-157	2
β-strand	158-163	6	1
β-strand	167-173	7	1
α-helix	174	1
β-strand	179	1	2
α-helix	180-187	8
α-helix	192-211	20
α-helix	221-223	3
β-strand	224-226	3	2
β-strand	232-234	3	2
α-helix	262-265	4
α-helix	273-288	16
α-helix	298-307	10
α-helix	318-327	10
α-helix	332-334	3
α-helix	343-347	5
α-helix	350-352	3
α-helix	357-361	5
α-helix	366-367	2
α-helix	371-373	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosomal protein S6 kinase beta-1	A	protein	329	Homo sapiens	P23443 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3WE4_1 Ribosomal protein S6 kinase beta-1 (chains A)
GSFTSSGSVNRGPEKIRPECFELLRVLGKGGYGKVFQVRKVTGANTGKIFAMKVLKKAMI
VRNAKDTAHTKAERNILEEVKHPFIVDLIYAFQTGGKLYLILEYLSGGELFMQLEREGIF
MEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDGTVT
HTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKL
NLPPYLTQEARDLLKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFK
PLLQSEEDVSQFDSKFTRQTPVDSPDDST

Ligands and cofactors

ID	Name	Formula	Copies
5FI	2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benz…	C19 H21 F3 N6	1
ZN	Zinc ion	Zn	1

Primary citation

Crystal structures of the S6K1 kinase domain in complexes with inhibitors. Niwa, H., Mikuni, J., Sasaki, S. et al. J Struct Funct Genomics (2014) 15:153-164. DOI 10.1007/s10969-014-9188-8 · PubMed

Other PDB entries of the same protein (UniProt P23443 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WBH 1.75 Å, Structure of the FRB domain of mTOR bound to a substrate recruitment peptide of S6K1
3WF7 1.85 Å, Crystal structure of S6K1 kinase domain in complex with a purine derivative…
3WF8 1.98 Å, Crystal structure of S6K1 kinase domain in complex with a quinoline derivative…
3WF6 2.03 Å, Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative…
3WF9 2.04 Å, Crystal structure of S6K1 kinase domain in complex with a quinoline derivative…
3WF5 2.1 Å, Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative…
4L3J 2.1 Å, Crystal structures of human p70S6K1 kinase domain
4L3L 2.1 Å, Crystal structures of human p70S6K1 kinase domain (Zinc anomalous)
3A62 2.35 Å, Crystal structure of phosphorylated p70S6K1
4RLO 2.53 Å, Human p70s6k1 with ruthenium-based inhibitor EM5
7N93 2.74 Å, P70 S6K1 in complex with MSC2363318A-1
4RLP 2.79 Å, Human p70s6k1 with ruthenium-based inhibitor FL772

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