3F3T

Kinase domain of cSrc in complex with inhibitor RL38 (Type III)

• PDB DOI: https://doi.org/10.2210/pdb3F3T/pdb

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


• Deposited: 2008-10-31 Released: 2009-03-03 
• Deposition Author(s): Gruetter, C., Klueter, S., Getlik, M., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.295 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

A new screening assay for allosteric inhibitors of cSrc

Simard, J.R., Kluter, S., Grutter, C., Getlik, M., Rabiller, M., Rode, H.B., Rauh, D.

(2009) Nat Chem Biol 5: 394-396

• PubMed: 19396179 
• DOI: https://doi.org/10.1038/nchembio.162
• Primary Citation of Related Structures:  
  3F3T, 3F3U


• PubMed Abstract: 
  

  Targeting kinases outside the highly conserved ATP pocket is thought to be a promising strategy for overcoming bottlenecks in kinase inhibitor research, such as limited selectivity and drug resistance. Here we report the development and application of a direct binding assay to detect small molecules that stabilize the inactive conformation of the tyrosine kinase cSrc. Protein X-ray crystallography validated the assay results and confirmed an exclusively allosteric binding mode.

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Organizational Affiliation: 

Chemical Genomics Centre of the Max Planck Society, 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: 4,347 
• Modelled Residue Count: 520 
• 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): 1  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
1AU	C [auth A], D [auth A]	1-[1-(3-aminophenyl)-3-tert-butyl-1H-pyrazol-5-yl]-3-naphthalen-1-ylurea C24 H25 N5 O HJWMLCDGRWWLAQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1AU	PDBBind:  3F3T	Kd: 2.60e+4 (nM) from 1 assay(s)
	BindingDB:  3F3T	IC50: 6.41e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.295 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.01	α = 78.71
b = 63.49	β = 89.71
c = 74.99	γ = 89.91

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Gruetter, C., Klueter, S., Getlik, M., Rauh, D.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description