5D9L | pdb_00005d9l

Rsk2 N-terminal Kinase in Complex with bis-phenol pyrazole

• PDB DOI: https://doi.org/10.2210/pdb5D9L/pdb

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-08-18 Released: 2015-09-02 
• Deposition Author(s): Appleton, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.224 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Discovery of Potent and Selective RSK Inhibitors as Biological Probes.

Jain, R., Mathur, M., Lan, J., Costales, A., Atallah, G., Ramurthy, S., Subramanian, S., Setti, L., Feucht, P., Warne, B., Doyle, L., Basham, S., Jefferson, A.B., Lindvall, M., Appleton, B.A., Shafer, C.M.

(2015) J Med Chem 58: 6766-6783

• PubMed: 26270416 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00450
• Primary Citation Related Structures: 
  5D9K, 5D9L


• PubMed Abstract: 
  

  While the p90 ribosomal S6 kinase (RSK) family has been implicated in multiple tumor cell functions, the full understanding of this kinase family has been restricted by the lack of highly selective inhibitors. A bis-phenol pyrazole was identified from high-throughput screening as an inhibitor of the N-terminal kinase of RSK2. Structure-based drug design using crystallography, conformational analysis, and scaffold morphing resulted in highly optimized difluorophenol pyridine inhibitors of the RSK kinase family as demonstrated cellularly by the inhibition of YB1 phosphorylation. These compounds provide for the first time in vitro tools with an improved selectivity and potency profile to examine the importance of RSK signaling in cancer cells and to fully evaluate RSK as a therapeutic target.

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Organizational Affiliation: 
• Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.55 kDa 
• Atom Count: 2,602 
• Modeled Residue Count: 299 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase alpha-3	A	323	Homo sapiens	Mutation(s): 0  Gene Names: RPS6KA3, ISPK1, MAPKAPK1B, RSK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P51812 (Homo sapiens) Explore P51812  Go to UniProtKB:  P51812
PHAROS:  P51812 GTEx:  ENSG00000177189

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
583	B [auth A]	4,4'-(1H-pyrazole-3,4-diyl)diphenol C15 H12 N2 O2 FHGTUVGVZRNUDB-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.224 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.45	α = 90
b = 58.59	β = 100.64
c = 78.57	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Appleton, B.A.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations