2E2B

Crystal structure of the c-Abl kinase domain in complex with INNO-406

• PDB DOI: https://doi.org/10.2210/pdb2E2B/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-11-10 Released: 2007-05-22 
• Deposition Author(s): Horio, T., Hamasaki, T., Wakayama, T., Takagaki, K., Ohgi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.236 

Starting Model: experimental

Literature

Structural factors contributing to the Abl/Lyn dual inhibitory activity of 3-substituted benzamide derivatives

Horio, T., Hamasaki, T., Inoue, T., Wakayama, T., Itou, S., Naito, H., Asaki, T., Hayase, H., Niwa, T.

(2007) Bioorg Med Chem Lett 17: 2712-2717

• PubMed: 17376680 
• DOI: https://doi.org/10.1016/j.bmcl.2007.03.002
• Primary Citation of Related Structures:  
  2E2B


• PubMed Abstract: 
  

  To investigate why 3-substituted benzamide derivatives show dual inhibition of Abl and Lyn protein tyrosine kinases, we determined their inhibitory activities against Abl and Lyn, carried out molecular modeling, and conducted a structure-activity relationship study with the aid of a newly determined X-ray structure of the Abl/Lyn dual inhibitor INNO-406 (formerly known as NS-187) bound to human Abl. We found that this series of compounds interacted with both kinases in very similar ways, so that they can inhibit both kinases effectively.

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Organizational Affiliation: 

Research Laboratories, Nippon Shinyaku Co. Ltd., 3-14-1 Sakura, Tsukuba, Ibaraki 305-0003, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.63 kDa 
• Atom Count: 4,545 
• Modelled Residue Count: 532 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase ABL1	A, B	293	Homo sapiens	Mutation(s): 0  EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens) Explore P00519  Go to UniProtKB:  P00519
GTEx:  ENSG00000097007

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
406	C [auth A], D [auth B]	N-[3-(4,5'-BIPYRIMIDIN-2-YLAMINO)-4-METHYLPHENYL]-4-{[(3S)-3-(DIMETHYLAMINO)PYRROLIDIN-1-YL]METHYL}-3-(TRIFLUOROMETHYL) BENZAMIDE C30 H31 F3 N8 O ZGBAJMQHJDFTQJ-DEOSSOPVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
406	PDBBind:  2E2B	IC50: 11 (nM) from 1 assay(s)
	BindingDB:  2E2B	IC50: min: 4, max: 26 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.236 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.82	α = 90
b = 147.58	β = 90
c = 152.49	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Horio, T., Hamasaki, T., Wakayama, T., Takagaki, K., Ohgi, T.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary