ABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 

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Binding or bending: distinction of allosteric Abl kinase agonists from antagonists by an NMR-based conformational assay.

Jahnke, W.Grotzfeld, R.M.Pelle, X.Strauss, A.Fendrich, G.Cowan-Jacob, S.W.Cotesta, S.Fabbro, D.Furet, P.Mestan, J.Marzinzik, A.L.

(2010) J Am Chem Soc 132: 7043-7048

  • DOI: https://doi.org/10.1021/ja101837n
  • Primary Citation of Related Structures:  
    3MS9, 3MSS

  • PubMed Abstract: 

    Allosteric inhibitors of Bcr-Abl have emerged as a novel therapeutic option for the treatment of CML. Using fragment-based screening, a search for novel Abl inhibitors that bind to the myristate pocket was carried out. Here we show that not all myristate ligands are functional inhibitors, but that the conformational state of C-terminal helix_I is a structural determinant for functional activity. We present an NMR-based conformational assay to monitor the conformation of this crucial helix_I and show that myristate ligands that bend helix_I are functional antagonists, whereas ligands that bind to the myristate pocket but do not induce this conformational change are kinase agonists. Activation of c-Abl by allosteric agonists has been confirmed in a biochemical assay.

  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland. wolfgang.jahnke@novartis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1
A, B
293Mus musculusMutation(s): 0 
Gene Names: Abl1Abl
Find proteins for P00520 (Mus musculus)
Explore P00520 
Go to UniProtKB:  P00520
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00520
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on STI

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
C29 H31 N7 O
Query on MS9

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
methyl 2-amino-4-chlorobenzoate
C8 H8 Cl N O2
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
STI BindingDB:  3MS9 Ki: min: 13, max: 7000 (nM) from 5 assay(s)
Kd: min: 1, max: 1.00e+4 (nM) from 35 assay(s)
IC50: min: 1.1, max: 1.00e+4 (nM) from 60 assay(s)
EC50: min: 34, max: 1000 (nM) from 4 assay(s)
MS9 PDBBind:  3MS9 Kd: 6000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.783α = 90
b = 147.346β = 90
c = 152.833γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Structure summary