2HIW

Crystal Structure of Inactive Conformation Abl Kinase Catalytic Domain Complexed with Type II Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A general strategy for creating

Okram, B.Nagle, A.Adrian, F.J.Lee, C.Ren, P.Wang, X.Sim, T.Xie, Y.Wang, X.Xia, G.Spraggon, G.Warmuth, M.Liu, Y.Gray, N.S.

(2006) Chem.Biol. 13: 779-786

  • DOI: 10.1016/j.chembiol.2006.05.015

  • PubMed Abstract: 
  • Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydr ...

    Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydrophobic site immediately adjacent to the ATP pocket made accessible by a conformational rearrangement of the activation loop (type II). To date, all type II inhibitors were discovered by using structure-activity-guided optimization strategies. Here, we describe a general pharmacophore model of type II inhibition that enables a rational "hybrid-design" approach whereby a 3-trifluoromethylbenzamide functionality is appended to four distinct type I scaffolds in order to convert them into their corresponding type II counterparts. We demonstrate that the designed compounds function as type II inhibitors by using biochemical and cellular kinase assays and by cocrystallography with Abl.


    Organizational Affiliation

    Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase ABL1
A, B
287Homo sapiensMutation(s): 0 
Gene Names: ABL1 (ABL, JTK7)
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to Gene View: ABL1
Go to UniProtKB:  P00519
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MP
Query on 7MP

Download SDF File 
Download CCD File 
A, B
7-AMINO-1-METHYL-3-(2-METHYL-5-{[3-(TRIFLUOROMETHYL)BENZOYL]AMINO}PHENYL)-2-OXO-2,3-DIHYDROPYRIMIDO[4,5-D]PYRIMIDIN-1-IUM
C22 H18 F3 N6 O2
SQOIIWIQKKMCCG-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7MPIC50: 8 nM BINDINGMOAD
7MPIC50: 8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.243 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 41.485α = 90.00
b = 41.485β = 90.00
c = 332.602γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-06-29 
  • Released Date: 2006-08-22 
  • Deposition Author(s): Lee, C.

Revision History 

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance