Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 38.31 kDa 
• Atom Count: 2673 
• Modelled Residue Count: 289 
• Deposited Residue Count: 329 
• Unique protein chains: 1

5U8L

Crystal structure of EGFR kinase domain in complex with a sulfonyl fluoride probe XO44

• PDB DOI: 10.2210/pdb5U8L/pdb

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


• Deposited: 2016-12-14 Released: 2017-01-25 
• Deposition Author(s): Gajiwala, K.S., Ferre, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes.

Zhao, Q., Ouyang, X., Wan, X., Gajiwala, K.S., Kath, J.C., Jones, L.H., Burlingame, A.L., Taunton, J.

(2017) J Am Chem Soc 139: 680-685

• PubMed: 28051857 
• DOI: 10.1021/jacs.6b08536
• Primary Citation of Related Structures:  
  5K9I, 5U8L


• PubMed Abstract: 
  

Protein kinases comprise a large family of structurally related enzymes. A major goal in kinase-inhibitor development is to selectively engage the desired kinase while avoiding myriad off-target kinases. However, quantifying inhibitor interactions with multiple endogenous kinases in live cells remains an unmet challenge. Here, we report the design of sulfonyl fluoride probes that covalently label a broad swath of the intracellular kinome with high efficiency. Protein crystallography and mass spectrometry confirmed a chemoselective reaction between the sulfonyl fluoride and a conserved lysine in the ATP binding site. Optimized probe 2 (XO44) covalently modified up to 133 endogenous kinases, efficiently competing with high intracellular concentrations of ATP. We employed probe 2 and label-free mass spectrometry to quantify intracellular kinase engagement by the approved drug, dasatinib. The data revealed saturable dasatinib binding to a small subset of kinase targets at clinically relevant concentrations, highlighting the utility of lysine-targeted sulfonyl fluoride probes in demanding chemoproteomic applications.

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Organizational Affiliation: 

Medicine Design, Pfizer , Cambridge, Massachusetts 02139, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	329	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
PHAROS:  P00533 GTEx:  ENSG00000146648

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O44	B [auth A]	4-[(4-{4-[(3-cyclopropyl-1H-pyrazol-5-yl)amino]-6-[(prop-2-yn-1-yl)carbamoyl]pyrimidin-2-yl}piperazin-1-yl)methyl]benzene-1-sulfonyl fluoride C25 H27 F N8 O3 S ZBSPMOBILDLOCV-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.364	α = 90
b = 69.977	β = 90
c = 110.403	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
XDS	data reduction
Aimless	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-14 
• Released Date: 2017-01-25 
Deposition Author(s): Gajiwala, K.S., Ferre, R.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Database references