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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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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.

(2014) J Struct Funct Genomics 15: 153-164

  • DOI: https://doi.org/10.1007/s10969-014-9188-8
  • Primary Citation of Related Structures:  
    3WE4, 3WF5, 3WF6, 3WF7, 3WF8, 3WF9

  • PubMed 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase beta-1329Homo sapiensMutation(s): 0 
Gene Names: RPS6KB1
UniProt & NIH Common Fund Data Resources
Find proteins for P23443 (Homo sapiens)
Explore P23443 
Go to UniProtKB:  P23443
PHAROS:  P23443
GTEx:  ENSG00000108443 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23443
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5FI

Download Ideal Coordinates CCD File 
C [auth A]2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole
C19 H21 F3 N6
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on TPO
Binding Affinity Annotations 
IDSourceBinding Affinity
5FI Binding MOAD:  3WE4 IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.93α = 90
b = 70.93β = 90
c = 146.861γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2014-10-29
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description