Biological Assembly 1  

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

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

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.64 kDa 
• Atom Count: 4337 
• Modelled Residue Count: 523 
• Deposited Residue Count: 562 
• Unique protein chains: 2

3U51

Src in complex with DNA-templated macrocyclic inhibitor MC1

• PDB DOI: 10.2210/pdb3U51/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-10 Released: 2012-02-22 
• Deposition Author(s): Seeliger, M.A., Liu, D.R., Georghiou, G., Kleiner, R.E., Pulkoski-Gross, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Highly specific, bisubstrate-competitive Src inhibitors from DNA-templated macrocycles.

Georghiou, G., Kleiner, R.E., Pulkoski-Gross, M., Liu, D.R., Seeliger, M.A.

(2012) Nat Chem Biol 8: 366-374

• PubMed: 22344177 
• DOI: 10.1038/nchembio.792
• Primary Citation of Related Structures:  
  3U4W, 3U51


• PubMed Abstract: 
  

Protein kinases are attractive therapeutic targets, but their high sequence and structural conservation complicates the development of specific inhibitors. We recently identified, in a DNA-templated macrocycle library, inhibitors with unusually high selectivity among Src-family kinases. Starting from these compounds, we developed and characterized in molecular detail potent macrocyclic inhibitors of Src kinase and its cancer-associated 'gatekeeper' mutant. We solved two cocrystal structures of macrocycles bound to Src kinase. These structures reveal the molecular basis of the combined ATP- and substrate peptide-competitive inhibitory mechanism and the remarkable kinase specificity of the compounds. The most potent compounds inhibit Src activity in cultured mammalian cells. Our work establishes that macrocycles can inhibit protein kinases through a bisubstrate-competitive mechanism with high potency and exceptional specificity, reveals the precise molecular basis for their desirable properties and provides new insights into the development of Src-specific inhibitors with potential therapeutic relevance.

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Organizational Affiliation: 

Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	275	Gallus gallus	Mutation(s): 0  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
macrocyclic inhibitor MC1	C, D	6	N/A	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC	C, D	L-PEPTIDE LINKING	C9 H17 N O2		ALA
DAB	C, D	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Binding Affinity Annotations
ID	Source	Binding Affinity
08X	Binding MOAD:  3U51	Kd: 3100 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001023	C, D	(2S,5S,8S,13S,16Z)-5-(cyclohexylmethyl)-3,6,9,15,18-pentaoxo-2-(3-phenylprop-2-en-1-yl)-8-{3-[(pyrazin-2-ylcarbonyl)amino]propyl}-1,4,7,10,14-pentaazacyclooctadec-16-ene-13-carboxamide	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.166	α = 90
b = 117.25	β = 90.08
c = 62.762	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-10 
• Released Date: 2012-02-22 
Deposition Author(s): Seeliger, M.A., Liu, D.R., Georghiou, G., Kleiner, R.E., Pulkoski-Gross, M.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references
• Version 1.2: 2012-04-04
  Changes: Database references
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2020-09-23
  Changes: Derived calculations