› 3we4

X-ray diffraction
2Å resolution

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

Released:
DOI: 10.2210/pdb3we4/pdb
PDB entry 3we4 coloured by chain, front view.
PDB entry 3we4 coloured by chain, side view.
PDB entry 3we4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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 15 153-64 (2014)
PMID: 25078151

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149961 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal protein S6 kinase beta-1 Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 37.18 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P23443 (Residues: 78-399; Coverage: 61%)
Gene names: RPS6KB1, STK14A
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand 5FI 1 x 5FI
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P41212
Unit cell:
a: 70.93Å b: 70.93Å c: 146.861Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.231
Expression system: Spodoptera frugiperda

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Citations

1 review citation

Towards Kinase Inhibitor Therapies for Fragile X Syndrome: Tweaking Twists in the Autism Spectrum Kinase Signaling Network.
D'Incal et al. (2022)
2 other articles

3 mentions without citation

Identification of a novel S6K1 inhibitor, rosmarinic acid methyl ester, for treating cisplatin-resistant cervical cancer.
Nam et al. (2019)
2 more