› 3wf5

X-ray diffraction
2.1Å resolution

Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine

Released:
DOI: 10.2210/pdb3wf5/pdb
PDB entry 3wf5 coloured by chain, front view.
PDB entry 3wf5 coloured by chain, side view.
PDB entry 3wf5 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 FZ8 1 x FZ8
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P41212
Unit cell:
a: 69.217Å b: 69.217Å c: 143.181Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.175 0.233
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)
4 other articles

2 mentions without citation

Crystal structures of the S6K1 kinase domain in complexes with inhibitors.
Niwa et al. (2014)
1 more