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.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.22 kDa 
• Atom Count: 3763 
• Modelled Residue Count: 484 
• Deposited Residue Count: 572 
• Unique protein chains: 1

2HWP

Crystal structure of Src kinase domain in complex with covalent inhibitor PD168393

• PDB DOI: 10.2210/pdb2HWP/pdb

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


• Deposited: 2006-08-01 Released: 2007-02-27 
• Deposition Author(s): Rauh, D., Blair, J.A., Shokat, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.276 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 

Literature

Structure-guided development of affinity probes for tyrosine kinases using chemical genetics.

Blair, J.A., Rauh, D., Kung, C., Yun, C.H., Fan, Q.W., Rode, H., Zhang, C., Eck, M.J., Weiss, W.A., Shokat, K.M.

(2007) Nat Chem Biol 3: 229-238

• PubMed: 17334377 
• DOI: 10.1038/nchembio866
• Primary Citation of Related Structures:  
  2HWO, 2HWP, 2J5E, 2J5F


• PubMed Abstract: 
  

As key components in nearly every signal transduction pathway, protein kinases are attractive targets for the regulation of cellular signaling by small-molecule inhibitors. We report the structure-guided development of 6-acrylamido-4-anilinoquinazoline irreversible kinase inhibitors that potently and selectively target rationally designed kinases bearing two selectivity elements that are not found together in any wild-type kinase: an electrophile-targeted cysteine residue and a glycine gatekeeper residue. Cocrystal structures of two irreversible quinazoline inhibitors bound to either epidermal growth factor receptor (EGFR) or engineered c-Src show covalent inhibitor binding to the targeted cysteine (Cys797 in EGFR and Cys345 in engineered c-Src). To accommodate the new covalent bond, the quinazoline core adopts positions that are different from those seen in kinase structures with reversible quinazoline inhibitors. Based on these structures, we developed a fluorescent 6-acrylamido-4-anilinoquinazoline affinity probe to report the fraction of kinase necessary for cellular signaling, and we used these reagents to quantitate the relationship between EGFR stimulation by EGF and its downstream outputs-Akt, Erk1 and Erk2.

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DJK	C [auth A], D [auth B]	N-[4-(3-BROMO-PHENYLAMINO)-QUINAZOLIN-6-YL]-ACRYLAMIDE C17 H13 Br N4 O HTUBKQUPEREOGA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DJK	BindingDB:  2HWP	IC50: min: 340, max: 2.70e+4 (nM) from 4 assay(s)
	PDBBind:  2HWP	IC50: 73 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.276 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.063	α = 100.74
b = 63.012	β = 89.81
c = 73.692	γ = 90.2

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-01 
• Released Date: 2007-02-27 
Deposition Author(s): Rauh, D., Blair, J.A., Shokat, K.M.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations