Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.89 kDa 
• Atom Count: 2423 
• Modelled Residue Count: 299 
• Deposited Residue Count: 342 
• Unique protein chains: 1

4D9T

Rsk2 C-terminal Kinase Domain with inhibitor (E)-methyl 3-(4-amino-7-(3-hydroxypropyl)-5-p-tolyl-7H-pyrrolo[2,3-d]pyrimidin-6-yl)-2-cyanoacrylate

• DOI: 10.2210/pdb4D9T/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-12 Released: 2012-04-25 
• Deposition Author(s): Serafimova, I.M., Pufall, M.A., Krishnan, S., Duda, K., Cohen, M.S., Maglathlin, R.L., McFarland, J.M., Miller, R.M., Frodin, M., Taunton, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.267 
• R-Value Work: 0.216 
• R-Value Observed: 0.221 

Literature

Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles.

Serafimova, I.M., Pufall, M.A., Krishnan, S., Duda, K., Cohen, M.S., Maglathlin, R.L., McFarland, J.M., Miller, R.M., Frodin, M., Taunton, J.

(2012) Nat Chem Biol 8: 471-476

• PubMed: 22466421 
• DOI: 10.1038/nchembio.925
• Primary Citation of Related Structures:  
  4D9T, 4D9U


• PubMed Abstract: 
  

Targeting noncatalytic cysteine residues with irreversible acrylamide-based inhibitors is a powerful approach for enhancing pharmacological potency and selectivity. Nevertheless, concerns about off-target modification motivate the development of reversible cysteine-targeting strategies. Here we show that electron-deficient olefins, including acrylamides, can be tuned to react with cysteine thiols in a rapidly reversible manner. Installation of a nitrile group increased the olefins' intrinsic reactivity, but, paradoxically, eliminated the formation of irreversible adducts. Incorporation of these electrophiles into a noncovalent kinase-recognition scaffold produced slowly dissociating, covalent inhibitors of the p90 ribosomal protein S6 kinase RSK2. A cocrystal structure revealed specific noncovalent interactions that stabilize the complex by positioning the electrophilic carbon near the targeted cysteine. Disruption of these interactions by protein unfolding or proteolysis promoted instantaneous cleavage of the covalent bond. Our results establish a chemistry-based framework for engineering sustained covalent inhibition without accumulating permanently modified proteins and peptides.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase alpha-3	A	342	Homo sapiens	Mutation(s): 0  Gene Names: ISPK1, MAPKAPK1B, RPS6KA3, RSK2 EC: 2.7.11.1
Find proteins for P51812 (Homo sapiens) Explore P51812  Go to UniProtKB:  P51812
NIH Common Fund Data Resources
PHAROS:  P51812 GTEx:  ENSG00000177189

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0JG	B [auth A]	methyl (2S)-3-{4-amino-7-[(1E)-3-hydroxyprop-1-en-1-yl]-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl}-2-cyanopropanoate C21 H21 N5 O3 ZJERBAYUHUAUBE-GZTQLTBSSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.267 
• R-Value Work: 0.216 
• R-Value Observed: 0.221 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.7	α = 90
b = 46.7	β = 90
c = 294.1	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: 2012-01-12 
• Released Date: 2012-04-25 
Deposition Author(s): Serafimova, I.M., Pufall, M.A., Krishnan, S., Duda, K., Cohen, M.S., Maglathlin, R.L., McFarland, J.M., Miller, R.M., Frodin, M., Taunton, J.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references