2G2H

A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A SRC-like inactive conformation in the abl tyrosine kinase domain.

Levinson, N.M., Kuchment, O., Shen, K., Young, M.A., Koldobskiy, M., Karplus, M., Cole, P.A., Kuriyan, J.

(2006) PLoS Biol 4: 753-767

  • DOI: 10.1371/journal.pbio.0040144
  • Primary Citation of Related Structures:  
    2G1T, 2G2I, 2G2H, 2G2F

  • PubMed Abstract: 

    • The improper activation of the Abl tyrosine kinase results in chronic myeloid leukemia (CML). The recognition of an inactive conformation of Abl, in which a catalytically important Asp-Phe-Gly (DFG) motif is flipped by approximately 180 degrees with respect to the active conformation, underlies the specificity of the cancer drug imatinib, which is used to treat CML ...

    The improper activation of the Abl tyrosine kinase results in chronic myeloid leukemia (CML). The recognition of an inactive conformation of Abl, in which a catalytically important Asp-Phe-Gly (DFG) motif is flipped by approximately 180 degrees with respect to the active conformation, underlies the specificity of the cancer drug imatinib, which is used to treat CML. The DFG motif is not flipped in crystal structures of inactive forms of the closely related Src kinases, and imatinib does not inhibit c-Src. We present a structure of the kinase domain of Abl, determined in complex with an ATP-peptide conjugate, in which the protein adopts an inactive conformation that resembles closely that of the Src kinases. An interesting aspect of the Src-like inactive structure, suggested by molecular dynamics simulations and additional crystal structures, is the presence of features that might facilitate the flip of the DFG motif by providing room for the phenylalanine to move and by coordinating the aspartate side chain as it leaves the active site. One class of mutations in BCR-Abl that confers resistance to imatinib appears more likely to destabilize the inactive Src-like conformation than the active or imatinib-bound conformations. Our results suggest that interconversion between distinctly different inactive conformations is a characteristic feature of the Abl kinase domain.

    Organizational Affiliation: 

    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Abl TyrosineA, B287Homo sapiensMutation(s): 1 
Gene Names: ABL1, ABL, JTK7
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS:  P00519
GTEx:  ENSG00000097007
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P16
Query on P16
Download Ideal Coordinates CCD File 
 C [auth A], D [auth B]6-(2,6-DICHLOROPHENYL)-2-{[3-(HYDROXYMETHYL)PHENYL]AMINO}-8-METHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
C21 H16 Cl2 N4 O2
ZIQFYVPVJZEOFS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P16IC50:  2.799999952316284   nM  BindingDB
P16Ki:  1000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.386α = 90
b = 131.487β = 90
c = 56.499γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance