Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.30 kDa 
• Atom Count: 2423 
• Modelled Residue Count: 302 
• Deposited Residue Count: 355 
• Unique protein chains: 1

4JG6

RSK2 CTD bound to 2-cyano-3-(1H-indazol-5-yl)acrylamide

• DOI: 10.2210/pdb4JG6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-28 Released: 2013-04-10 
• Deposition Author(s): Miller, R.M., Paavilainen, V.O., Krishnan, S., Serafimova, I.M., Taunton, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.299 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 

Literature

Electrophilic fragment-based design of reversible covalent kinase inhibitors.

Miller, R.M., Paavilainen, V.O., Krishnan, S., Serafimova, I.M., Taunton, J.

(2013) J Am Chem Soc 135: 5298-5301

• PubMed: 23540679 
• DOI: 10.1021/ja401221b
• Primary Citation of Related Structures:  
  4JG6, 4JG7, 4JG8


• PubMed Abstract: 
  

Fragment-based ligand design and covalent targeting of noncatalytic cysteines have been employed to develop potent and selective kinase inhibitors. Here, we combine these approaches, starting with a panel of low-molecular-weight, heteroaryl-susbstituted cyanoacrylamides, which we have previously shown to form reversible covalent bonds with cysteine thiols. Using this strategy, we identify electrophilic fragments with sufficient ligand efficiency and selectivity to serve as starting points for the first reported inhibitors of the MSK1 C-terminal kinase domain. Guided by X-ray co-crystal structures, indazole fragment 1 was elaborated to afford 12 (RMM-46), a reversible covalent inhibitor that exhibits high ligand efficiency and selectivity for MSK/RSK-family kinases. At nanomolar concentrations, 12 blocked activation of cellular MSK and RSK, as well as downstream phosphorylation of the critical transcription factor, CREB.

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Organizational Affiliation: 

Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94158, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase alpha-3	A	355	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
1LB	B [auth A]	(2S)-2-cyano-3-(1H-indazol-5-yl)propanamide C11 H10 N4 O LSZLZUAHIJIGOY-QMMMGPOBSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1LB	IC50 :  360   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.299 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.28	α = 90
b = 47.28	β = 90
c = 291.97	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-28 
• Released Date: 2013-04-10 
Deposition Author(s): Miller, R.M., Paavilainen, V.O., Krishnan, S., Serafimova, I.M., Taunton, J.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2013-04-17
  Changes: Database references
• Version 1.2: 2013-04-24
  Changes: Database references