4RLO: Human p70s6k1 with ruthenium-based inhibitor EM5

Human p70s6k1 with ruthenium-based inhibitor EM5. Determined by X-ray diffraction at 2.53 Å resolution. Released 21 Jan 2015.

Method: X-ray diffraction
Resolution: 2.53 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,236
Mol. weight: 67.27 kDa
Ligands: STU, 3T3
Released: 21 Jan 2015

Explore 4RLO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RLO contains 28 α-helices and 23 β-strands across 2 chains. 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: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	88-90	3
β-strand	91-99	9	1
β-strand	104-110	7	1
β-strand	119-125	7	1
α-helix	143-149	7
β-strand	155	1	2
β-strand	158-163	6	1
β-strand	168-173	6	1
β-strand	178-179	2	2
α-helix	181-187	7
α-helix	192-211	20
β-strand	215	1	3
β-strand	224-226	3	2
β-strand	232-234	3	2
β-strand	241	1	3
α-helix	262-265	4
α-helix	273-288	16
α-helix	298-307	10
α-helix	308-310	3
α-helix	318-327	10
α-helix	343-347	5
α-helix	350-352	3
α-helix	357-361	5
α-helix	366-367	2

Chain B: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	88-90	3
β-strand	91-100	10	4
β-strand	103-110	8	4
β-strand	119-125	7	4
β-strand	155	1	5
α-helix	156-157	2
β-strand	158-164	7	4
β-strand	167-173	7	4
β-strand	177	1	6
α-helix	180-186	7
α-helix	192-211	20
β-strand	214-215	2	7
α-helix	221-223	3
β-strand	225-226	2	6
β-strand	232-233	2	6
β-strand	234	1	5
β-strand	242-243	2	7
α-helix	262-265	4
α-helix	273-288	16
α-helix	298-307	10
α-helix	308-310	3
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosomal protein S6 kinase beta-1	A, B	protein	288	Homo sapiens	P23443 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4RLO_1 Ribosomal protein S6 kinase beta-1 (chains A, B)
KIRPECFELLRVLGKGGYGKVFQVRKVTGANTGKIFAMKVLKKAMIVRNAKDTAHTKAER
NILEEVKHPFIVDLIYAFQTGGKLYLILEYLSGGELFMQLEREGIFMEDTACFYLAEISM
ALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDGTVTHTFCGTIEYMAPEI
LMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKLNLPPYLTQEARDLL
KKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPL

Ligands and cofactors

ID	Name	Formula	Copies
STU	Staurosporine	C28 H26 N4 O3	1
3T3	[(amino-kappaN)methanethiolato](3-fluoro-9-hydroxypyrido[2,3-a]pyrrolo[3,4-c]ca…	C24 H22 F N4 O3 Ru S4	1

Water and common crystallization additives (DMS, SO4, CL, GOL) are not listed.

Primary citation

Development of Organometallic S6K1 Inhibitors. Qin, J., Rajaratnam, R., Feng, L. et al. J Med Chem (2015) 58:305-314. DOI 10.1021/jm5011868 · 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…
3WE4 2.0 Å, Crystal structure of S6K1 kinase domain in complex with a pyrimidine 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
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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