Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.6 kDa 
• Atom Count: 4,253 
• Modelled Residue Count: 509 
• Deposited Residue Count: 572 
• Unique protein chains: 1

 5D11

Kinase domain of cSrc in complex with RL235

• PDB DOI:  https://doi.org/10.2210/pdb5D11/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-03 Released: 2015-09-09 
• Deposition Author(s): Becker, C., Gruetter, C., Engel, J., Rauh, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach.

Engel, J., Richters, A., Getlik, M., Tomassi, S., Keul, M., Termathe, M., Lategahn, J., Becker, C., Mayer-Wrangowski, S., Grutter, C., Uhlenbrock, N., Krull, J., Schaumann, N., Eppmann, S., Kibies, P., Hoffgaard, F., Heil, J., Menninger, S., Ortiz-Cuaran, S., Heuckmann, J.M., Tinnefeld, V., Zahedi, R.P., Sos, M.L., Schultz-Fademrecht, C., Thomas, R.K., Kast, S.M., Rauh, D.

(2015) J Med Chem 58: 6844-6863

• PubMed: 26275028 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01082
• Primary Citation of Related Structures:  
  5D10, 5D11, 5D12


• PubMed Abstract: 
  

Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797.

---

Organizational Affiliation: 

Chemical Genomics Centre of the Max-Planck Society , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 2  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
56G	D [auth A], F [auth B]	N-[3-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide C22 H26 N8 O2 PSWJMRDJPWAQDI-UHFFFAOYSA-N
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
56G	BindingDB:  5D11	IC50: min: 28, max: 170 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.12	α = 78.65
b = 63.43	β = 89.55
c = 75.35	γ = 90.29

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Becker, C., Gruetter, C., Engel, J., Rauh, D.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references