3LOK | pdb_00003lok

Drug resistant cSrc kinase domain in complex with covalent inhibitor PD168393

• PDB DOI: https://doi.org/10.2210/pdb3LOK/pdb

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


• Deposited: 2010-02-04 Released: 2010-12-22 
• Deposition Author(s): Gruetter, C., Rode, H.B., Rauh, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.286 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Characterization of irreversible kinase inhibitors by directly detecting covalent bond formation: a tool for dissecting kinase drug resistance

Klueter, S., Simard, J.R., Rode, H.B., Gruetter, C., Pawar, V., Raaijmakers, H.C., Barf, T.A., Rabiller, M., van Otterlo, W.A.L., Rauh, D.

(2010) Chembiochem 11: 2557-2566

• PubMed: 21080395 
• DOI: https://doi.org/10.1002/cbic.201000352
• Primary Citation Related Structures: 
  3LOK


• PubMed Abstract: 
  

  Targeting protein kinases in cancer therapy with irreversible small-molecule inhibitors is moving to the forefront of kinase-inhibitor research and is thought to be an effective means of overcoming mutation-associated drug resistance in epidermal growth factor receptor kinase (EGFR). We generated a detection technique that allows direct measurements of covalent bond formation without relying on kinase activity, thereby allowing the straightforward investigation of the influence of steric clashes on covalent inhibitors in different resistant kinase mutants. The obtained results are discussed together with structural biology and biochemical studies of catalytic activity in both wild-type and gatekeeper mutated kinase variants to draw conclusions about the impact of steric hindrance and increased catalytic activity in drug-resistant kinase variants.

---

Organizational Affiliation: 
• Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.28 kDa 
• Atom Count: 4,018 
• Modeled Residue Count: 490 
• Deposited Residue Count: 572 
• Unique protein chains: 1

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, v-Src sarcoma viral oncogene 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:  3LOK	IC50: min: 340, max: 2.70e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.286 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.09	α = 78.49
b = 63.26	β = 88.33
c = 74.22	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Gruetter, C., Rode, H.B., Rauh, D.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary