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 and generated by PISA (software)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.42 kDa 
• Atom Count: 3927 
• Modelled Residue Count: 486 
• Deposited Residue Count: 540 
• Unique protein chains: 1

4LGG

Structure of 3MB-PP1 bound to analog-sensitive Src kinase

• PDB DOI: 10.2210/pdb4LGG/pdb

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


• Deposited: 2013-06-27 Released: 2013-08-07 
• Deposition Author(s): Lopez, M.S., Dar, A.C., Shokat, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.285 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 

Literature

Structure-guided inhibitor design expands the scope of analog-sensitive kinase technology.

Zhang, C., Lopez, M.S., Dar, A.C., Ladow, E., Finkbeiner, S., Yun, C.H., Eck, M.J., Shokat, K.M.

(2013) ACS Chem Biol 8: 1931-1938

• PubMed: 23841803 
• DOI: 10.1021/cb400376p
• Primary Citation of Related Structures:  
  4LGG, 4LGH


• PubMed Abstract: 
  

Engineered analog-sensitive (AS) protein kinases have emerged as powerful tools for dissecting phospho-signaling pathways, for elucidating the cellular function of individual kinases, and for deciphering unanticipated effects of clinical therapeutics. A crucial and necessary feature of this technology is a bioorthogonal small molecule that is innocuous toward native cellular systems but potently inhibits the engineered kinase. In order to generalize this method, we sought a molecule capable of targeting divergent AS-kinases. Here we employ X-ray crystallography and medicinal chemistry to unravel the mechanism of current inhibitors and use these insights to design the most potent, selective, and general AS-kinase inhibitors reported to date. We use large-scale kinase inhibitor profiling to characterize the selectivity of these molecules as well as examine the consequences of potential off-target effects in chemical genetic experiments. The molecules reported here will serve as powerful tools in efforts to extend AS-kinase technology to the entire kinome and the principles discovered may help in the design of other engineered enzyme/ligand pairs.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Cellular & Molecular Pharmacology, University of California, San Francisco , San Francisco, California 94158, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	270	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
VGG	C [auth A], D [auth B]	1-tert-butyl-3-(3-methylbenzyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C17 H21 N5 FYCOTGCSHZKHPR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VGG	Binding MOAD:  4LGG	IC50: 3 (nM) from 1 assay(s)
	PDBBind:  4LGG	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.285 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.988	α = 89.98
b = 55.815	β = 90.06
c = 62.978	γ = 88.86

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-27 
• Released Date: 2013-08-07 
Deposition Author(s): Lopez, M.S., Dar, A.C., Shokat, K.M.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description